Targeted disruption of the mhc cell receptor

ABSTRACT

Disclosed herein are methods and compositions for inactivating MHC genes, using zinc finger nucleases (ZFNs) comprising a zinc finger protein and a cleavage domain or cleavage half-domain in conditions able to preserve cell viability. Polynucleotides encoding ZFNs, vectors comprising polynucleotides encoding ZFNs and cells comprising polynucleotides encoding ZFNs and/or cells comprising ZFNs are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 16/680,935, filed Nov. 12, 2019, which is a divisional of U.S.patent application Ser. No. 15/380,723, filed Dec. 15, 2016, now U.S.Pat. No. 10,500,229, which claims the benefit of U.S. ProvisionalApplication No. 62/269,410, filed Dec. 18, 2015; U.S. Provisional No.62/305,097, filed Mar. 8, 2016; and U.S. Provisional No. 62/329,439,filed Apr. 29, 2016, the disclosures of which are hereby incorporated byreference in their entireties.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy is named 128687-2821_SL.txtand is 52,363 bytes in size.

TECHNICAL FIELD

The present disclosure is in the field of genome modification of humancells, including lymphocytes and stem cells.

BACKGROUND

Gene therapy holds enormous potential for a new era of humantherapeutics. These methodologies will allow treatment for conditionsthat have not been addressable by standard medical practice. Genetherapy can include the many variations of genome editing techniquessuch as disruption or correction of a gene locus, and insertion of anexpressible transgene that can be controlled either by a specificexogenous promoter fused to the transgene, or by the endogenous promoterfound at the site of insertion into the genome.

Delivery and insertion of the transgene are examples of hurdles thatmust be solved for any real implementation of this technology. Forexample, although a variety of gene delivery methods are potentiallyavailable for therapeutic use, all involve substantial tradeoffs betweensafety, durability and level of expression. Methods that provide thetransgene as an episome (e.g. basic adenovirus (Ad), adeno-associatedvirus (AAV) and plasmid-based systems) are generally safe and can yieldhigh initial expression levels, however, these methods lack robustepisomal replication, which may limit the duration of expression inmitotically active tissues. In contrast, delivery methods that result inthe random integration of the desired transgene (e.g. integratinglentivirus (LV)) provide more durable expression but, due to theuntargeted nature of the random insertion, may provoke unregulatedgrowth in the recipient cells, potentially leading to malignancy viaactivation of oncogenes in the vicinity of the randomly integratedtransgene cassette. Moreover, although transgene integration avoidsreplication-driven loss, it does not prevent eventual silencing of theexogenous promoter fused to the transgene. Over time, such silencingresults in reduced transgene expression for the majority of non-specificinsertion events. In addition, integration of a transgene rarely occursin every target cell, which can make it difficult to achieve a highenough expression level of the transgene of interest to achieve thedesired therapeutic effect.

In recent years, a new strategy for transgene integration has beendeveloped that uses cleavage with site-specific nucleases (e.g., zincfinger nucleases (ZFNs), transcription activator-like effector domainnucleases (TALENs), CRISPR/Cas system with an engineered crRNA/tracr RNA(‘single guide RNA’), and the Cfp1/CRISPR system to guide specificcleavage, etc.) to bias insertion into a chosen genomic locus. See,e.g., U.S. Pat. Nos. 9,255,250; 9,045,763; 9,005,973; 8,956,828;8,945,868; 8,703,489; 8,586,526; 6,534,261; 6,599,692; 6,503,717;6,689,558; 7,067,317; 7,262,054; 7,888,121; 7,972,854; 7,914,796;7,951,925; 8,110,379; and 8,409,861; U.S. Patent Publication Nos.2003/0232410; 2005/0208489; 2005/0026157; 2005/0064474; 2006/0063231;2008/0159996; 2010/0218264; 2012/0017290; 2011/0265198; 2013/0137104;2013/0122591; 2013/0177983; 2013/0177960; and 20150056705. Further,targeted nucleases are being developed based on the Argonaute system(e.g., from T. thermophilus, known as ‘TtAgo’, see Swarts et al. (2014)Nature 507(7491):258-261), which also may have the potential for uses ingenome editing and gene therapy. This nuclease-mediated approach totransgene integration offers the prospect of improved transgeneexpression, increased safety and expressional durability, as compared toclassic integration approaches, since it allows exact transgenepositioning for a minimal risk of gene silencing or activation of nearbyoncogenes.

The T cell receptor (TCR) is an essential part of the selectiveactivation of T cells. Bearing some resemblance to an antibody, theantigen recognition part of the TCR is typically made from two chains, αand β, which co-assemble to form a heterodimer. The antibody resemblancelies in the manner in which a single gene encoding a TCR alpha and betacomplex is put together. TCR alpha (TCR α) and beta (TCR β) chains areeach composed of two regions, a C-terminal constant region and anN-terminal variable region. The genomic loci that encode the TCR alphaand beta chains resemble antibody encoding loci in that the TCR α genecomprises V and J segments, while the β chain locus comprises D segmentsin addition to V and J segments. For the TCR β locus, there areadditionally two different constant regions that are selected fromduring the selection process. During T cell development, the varioussegments recombine such that each T cell comprises a unique TCR variableportion in the alpha and beta chains, called the complementaritydetermining region (CDR), and the body has a large repertoire of T cellswhich, due to their unique CDRs, are capable of interacting with uniqueantigens displayed by antigen presenting cells. Once a TCR α or β generearrangement has occurred, the expression of the second correspondingTCR α or TCR β is repressed such that each T cell only expresses oneunique TCR structure in a process called ‘antigen receptor allelicexclusion’ (see Brady et al. (2010) J Immunol 185:3801-3808).

During T cell activation, the TCR interacts with antigens displayed aspeptides on the major histocompatability complex (MHC) of an antigenpresenting cell. Recognition of the antigen-MHC complex by the TCR leadsto T cell stimulation, which in turn leads to differentiation of both Thelper cells (CD4+) and cytotoxic T lymphocytes (CD8+) in memory andeffector lymphocytes. These cells then can expand in a clonal manner togive an activated subpopulation within the whole T cell populationcapable of reacting to one particular antigen.

MHC proteins are of two classes, I and II. The class I MHC proteins areheterodimers of two proteins, the α chain, which is a transmembraneprotein encoded by the MHC1 class I genes, and the β2 microglobulinchain (sometimes referred to as B2M), which is a small extracellularprotein that is encoded by a gene that does not lie within the MHC genecluster. The α chain folds into three globular domains and when the β2microglobulin chain is associated, the globular structure complex issimilar to an antibody complex. The foreign peptides are presented onthe two most N-terminal domains which are also the most variable. ClassII MHC proteins are also heterodimers, but the heterodimers comprise twotransmembrane proteins encoded by genes within the MHC complex. Theclass I MHC:antigen complex interacts with cytotoxic T cells while theclass II MHC presents antigens to helper T cells. In addition, class IMHC proteins tend to be expressed in nearly all nucleated cells andplatelets (and red blood cells in mice) while class II MHC protein aremore selectively expressed. Typically, class II MHC proteins areexpressed on B cells, some macrophage and monocytes, Langerhans cells,and dendritic cells.

The class I HLA gene cluster in humans comprises three major loci, B, Cand A, as well as several minor loci (including E, G and F, all found inthe HLA region on chromosome 6). The class II HLA cluster also comprisesthree major loci, DP, DQ and DR, and both the class I and class II geneclusters are polymorphic, in that there are several different alleles ofboth the class I and II genes within the population. There are alsoseveral accessory proteins that play a role in HLA functioning as well.β-2 microglobulin functions as a chaperon (encoded by B2M, located onchromosome 15) and stabilizes the HLA A, B or C protein expressed on thecell surface and also stabilizes the antigen display groove on the classI structure. It is found in the serum and urine in low amounts normally.

HLA plays a major role in transplant rejection. The acute phase oftransplant rejection can occur within about 1-3 weeks and usuallyinvolves the action of host T lymphocytes on donor tissues due tosensitization of the host system to the donor class I and class II HLAmolecules. In most cases, the triggering antigens are the class I HLAs.For best success, donors are typed for HLA and matched to the patientrecipient as completely as possible. But donation even between familymembers, which can share a high percentage of HLA identity, is stilloften not successful. Thus, in order to preserve the graft tissue withinthe recipient, the patient often must be subjected to profoundimmunosuppressive therapy to prevent rejection. Such therapy can lead tocomplications and significant morbidities due to opportunisticinfections that the patient may have difficulty overcoming. Regulationof the class I or II genes can be disrupted in the presence of sometumors and such disruption can have consequences on the prognosis of thepatients. For example, reduction of B2M expression was found inmetastatic colorectal cancers (Shrout et al. (2008) Br J Canc 98:1999).Since B2M has a key role in stabilizing the MHC class I complex, loss ofB2M in certain solid cancers has been hypothesized to be a mechanism ofimmune escape from T cell driven immune surveillance. Depressed B2Mexpression has been shown to be a result of suppression of the normalIFN gamma B2M expressional regulation and/or specific mutations in theB2M coding sequence that result in gene knock-out (Shrout et al., ibid).Confoundingly, increased B2M is also associated with some types ofcancer. Increased B2M levels in the urine serves as a prognosticator forseveral cancers including prostate, chronic lymphocytic leukemia (CLL)and Non-Hodgkin's lymphomas.

Adoptive cell therapy (ACT) is a developing form of cancer therapy basedon delivering tumor-specific immune cells to a patient in order for thedelivered cells to attack and clear the patient's cancer. ACT caninvolve the use of tumor-infiltrating lymphocytes (TILs) which areT-cells that are isolated from a patient's own tumor masses and expandedex vivo to re-infuse back into the patient. This approach has beenpromising in treating metastatic melanoma, where in one study, a longterm response rate of >50% was observed (see for example, Rosenberg etal. (2011) Clin Canc Res 17(13):4550). TILs are a promising source ofcells because they are a mixed set of the patient's own cells that haveT-cell receptors (TCRs) specific for the Tumor associated antigens(TAAs) present on the tumor (Wu et al. (2012) Cancer J 18(2):160). Otherapproaches involve editing T cells isolated from a patient's blood suchthat they are engineered to be responsive to a tumor in some way (Kaloset al. (2011) Sci Transl Med 3(95):95ra73).

Chimeric Antigen Receptors (CARs) are molecules designed to targetimmune cells to specific molecular targets expressed on cell surfaces.In their most basic form, they are receptors introduced into a cell thatcouple a specificity domain expressed on the outside of the cell tosignaling pathways on the inside of the cell such that when thespecificity domain interacts with its target, the cell becomesactivated. Often CARs are made from emulating the functional domains ofT-cell receptors (TCRs) where an antigen specific domain, such as a scFvor some type of receptor, is fused to the signaling domain, such asITAMs and other co-stimulatory domains. These constructs are thenintroduced into a T-cell ex vivo allowing the T-cell to become activatedin the presence of a cell expressing the target antigen, resulting inthe attack on the targeted cell by the activated T-cell in a non-MHCdependent manner (see Chicaybam et al. (2011) Int Rev Immunol30:294-311, Kalos, ibid) when the T-cell is re-introduced into thepatient. Thus, adoptive cell therapy using T cells altered ex vivo withan engineered TCR or CAR is a very promising clinical approach forseveral types of diseases. For example, cancers and their antigens thatare being targeted includes follicular lymphoma (CD20 or GD2),neuroblastoma (CD171), non-Hodgkin lymphoma (CD19 and CD20), lymphoma(CD19), glioblastoma (IL13Rα2), chronic lymphocytic leukemia or CLL andacute lymphocytic leukemia or ALL (both CD19). Virus specific CARs havealso been developed to attack cells harboring virus such as HIV. Forexample, a clinical trial was initiated using a CAR specific for Gp100for treatment of HIV (Chicaybam, ibid).

ACTRs (Antibody-coupled T-cell Receptors) are engineered T cellcomponents that are capable of binding to an exogenously suppliedantibody. The binding of the antibody to the ACTR component arms the Tcell to interact with the antigen recognized by the antibody, and whenthat antigen is encountered, the ACTR comprising T cell is triggered tointeract with antigen (see U.S. Patent Publication No. 2015/0139943).

One of the drawbacks of adoptive cell therapy however is the source ofthe cell product must be patient specific (autologous) to avoidpotential rejection of the transplanted cells. This has led researchersto develop methods of editing a patient's own T cells to avoid thisrejection. For example, a patient's T cells or hematopoietic stem cellscan be manipulated ex vivo with the addition of an engineered CAR, ACTRand/or T cell receptor (TCR), and then further treated with engineerednucleases to knock out T cell check point inhibitors such as PD1 and/orCTLA4 (see International Patent Publication No. WO 2014/059173). Forapplication of this technology to a larger patient population, it wouldbe advantageous to develop a universal population of cells (allogeneic).In addition, knockout of the TCR will result in cells that are unable tomount a graft-versus-host disease (GVHD) response once introduced into apatient.

Thus, there remains a need for methods and compositions that can be usedto modify MHC gene expression (e.g., knockout B2M) and/or knock out TCRexpression in T cells.

SUMMARY

Disclosed herein are compositions and methods for partial or completeinactivation or disruption of a B2M gene and compositions and methodsfor introducing and expressing to desired levels of exogenous TCR, CARor ACTR transgenes in T lymphocytes, after or simultaneously with thedisruption of an endogenous TCR and/or B2M. Additionally, providedherein are methods and compositions for deleting (inactivating) orrepressing a B2M gene to produce HLA class I null T cell, stem cell,tissue or whole organism, for example a cell that does not express oneor more HLA receptors on its surface. In certain embodiments, the HLAnull cells or tissues are human cells or tissues that are advantageousfor use in transplants. In preferred embodiments, the HLC null T cellsare prepared for use in adoptive T cell therapy.

In one aspect, described herein is an isolated cell (e.g., a eukaryoticcell such as a mammalian cell including a lymphoid cell, a stem cell(e.g., iPSC, embryonic stem cell, MSC or HSC), or a progenitor cell) inwhich expression of a beta 2 microglobulin (B2M) gene is modulated bymodification of exon 1 or exon 2 of the B2M gene. In certainembodiments, the modification is to a sequence as shown in one or moreof SEQ ID NO:6-48 or 137 to 205; within 1-5, within 1-10 or within 1-20base pairs on either side (the flanking genomic sequence) of SEQ IDNO:6-48 or 137 to 205; or within GGCCTTA, TCAAAT, TCAAATT, TTACTGAand/or AATTGAA. The modification may be by an exogenous fusion moleculecomprising a functional domain (e.g., transcriptional regulatory domain,nuclease domain) and a DNA-binding domain, including, but not limitedto: (i) a cell comprising an exogenous transcription factor comprising aDNA-binding domain that binds to a target site as shown in any of SEQ IDNO:6-48 or 137 to 205 and a transcriptional regulatory domain in whichthe transcription factor modifies B2M gene expression and/or (ii) a cellcomprising an insertion and/or a deletion within one or more of SEQ IDNO:6-48 or 137 to 205; within 1-5, within 1-10 or within 1-20 base pairson either side (the flanking genomic sequence) of SEQ ID NO:6-48 or 137to 205; or within GGCCTTA, TCAAAT, TCAAATT, TTACTGA and/or AATTGAA. Thecell may include further modifications, for example an inactivatedT-cell receptor gene, PD1 and/or CTLA4 gene and/or a transgene atransgene encoding a chimeric antigen receptor (CAR), a transgeneencoding an Antibody-coupled T-cell Receptor (ACTR) and/or a transgeneencoding an antibody. Pharmaceutical compositions comprising any cell asdescribed herein are also provided as well as methods of using the cellsand pharmaceutical compositions in ex vivo therapies for the treatmentof a disorder (e.g., a cancer) in a subject.

Thus, in one aspect, described herein are cells in which the expressionof a B2M gene is modulated (e.g., activated, repressed or inactivated).In preferred embodiments, exon 1 or exon 2 of the B2M is modulated. Themodulation may be by an exogenous molecule (e.g., engineeredtranscription factor comprising a DNA-binding domain and atranscriptional activation or repression domain) that binds to the B2Mgene and regulates B2M expression and/or via sequence modification ofthe B2M gene (e.g., using a nuclease that cleaves the B2M gene andmodifies the gene sequence by insertions and/or deletions). In certainembodiments, expression of one or more additional genes is alsomodulated (e.g., a TCR gene such as a TCRA gene). In some embodiments,cells are described that comprise an engineered nuclease to cause aknockout of a B2M gene such that the class I HLA complex isdestabilized. In preferred embodiments, the destabilization of the classI HLA results in a marked loss of class I HLA complex on the surface ofa cell. In other embodiments, cells are described that comprise anexogenous molecule, for instance an engineered transcription factor(TF), such that the expression of a B2M gene is modulated. In someembodiments, the cells are T cells. Further described are cells whereinthe expression of a B2M gene is modulated and wherein the cells arefurther engineered to comprise a least one exogenous transgene or anadditional knock out of at least one endogenous gene or combinationsthereof. The exogenous transgene may be integrated into a TCR gene(e.g., when the TCR gene is knocked out), may be integrated into a B2Mgene and/or may be integrated into a non-TCR, non-B2M locus such as asafe harbor locus. In some cases, the exogenous transgene encodes anACTR, an engineered TCR and/or a CAR. The transgene construct may beinserted by either HDR- or NHEJ-driven processes. In some aspects thecells with modulated B2M expression lack significant class I HLA ontheir cell surface, and further comprise at least an exogenous ACTRand/or an exogenous CAR. Some cells comprising a B2M modulator furthercomprise a knockout of one or more check point inhibitor genes. In someembodiments, the check point inhibitor is PD1. In other embodiments, thecheck point inhibitor is CTLA4. In further aspects, the B2M modulatedcell comprises a PD1 knockout and a CTLA4 knockout. In some embodiments,the cell is further modified at a TCR gene. In some embodiments, the TCRgene modulated is a gene encoding TCR β (TCRB). In some embodiments thisis achieved via targeted cleavage of the constant region of this gene(TCR β Constant region, or TRBC). In certain embodiments, the TCR genemodulated is a gene encoding TCR α (TCRA). In further embodiments,insertion is achieved via targeted cleavage of the constant region of aTCR gene, including targeted cleavage of the constant region of a TCR αgene (referred to herein as “TRAC” sequences). In some embodiments, theB2M-gene modified cells are further modified at a TCR gene, the HLA-A,-B, -C genes, or the TAP gene, or any combination thereof. In otherembodiments, the regulator for HLA class II, CTIIA, is also modified.

In certain embodiments, the cells described herein comprise amodification (e.g., deletion and/or insertion, binding of an engineeredTF to repress B2M) to a B2M gene (e.g., modification of exon 1 or exon2). In certain embodiments, the modification is of SEQ ID NO:6-48 and/or137-205, including modification by binding to, cleaving, insertingand/or deleting one or more nucleotides within any of these sequencesand/or within 1-50 base pairs (including any value therebetween such as1-5, 1-10 or 1-20 base pairs) of the gene (genomic) sequences flankingthese sequences in the B2M gene. In certain embodiments, the cellscomprise a modification (binding to, cleaving, insertions and/ordeletions) within one or more of the following sequences: GGCCTTA,TCAAATT, TCAAAT, TTACTGA and/or AATTGAA within a B2M gene (e.g., exon 1and/or 2, see FIG. 1). In certain embodiments, the modificationcomprises binding of an engineered TF as described herein such that B2Mexpression is modulated, for example, repressed or activated. In otherembodiments, the modification is a genetic modification (alteration ofnucleotide sequence) at or near nuclease(s) binding (target) and/orcleavage site(s), including but not limited to, modifications tosequences within 1-300 (or any number of base pairs therebetween) basepairs upstream, downstream and/or including 1 or more base pairs of thesite(s) of cleavage and/or binding site; modifications within 1-100 basepairs (or any number of base pairs therebetween) of including and/or oneither side of the binding and/or cleavage site(s); modifications within1 to 50 base pairs (or any number of base pairs therebetween) includingand/or on either side (e.g., 1 to 5, 1 to 10, 1-20 or more base pairs)of the binding and/or cleavage site(s); and/or modifications to one ormore base pairs within the nuclease binding site and/or cleavage site.In certain embodiments, the modification is at or near (e.g., 1-300,1-50, 1-20, 1-10 or 1-5 or more) base pairs or any number of base pairstherebetween) of the B2M gene sequence surrounding any of SEQ IDNOs:6-48 or 137-205. In certain embodiments, the modification includesmodifications of a B2M gene within one or more of the sequences shown inSEQ ID NOs:6 to 48 or 137 through 205 or within GGCCTTA, TCAAATT,TCAAAT, TTACTGA and/or AATTGAA of a B2M gene (e.g., exon 1 and/or exon2), for example a modification of 1 or more base pairs to one or more ofthese sequences. In certain embodiments, the nuclease-mediated geneticmodifications are between paired target sites (when a dimer is used tocleave the target). The nuclease-mediated genetic modifications mayinclude insertions and/or deletions of any number of base pairs,including insertions of non-coding sequences of any length and/ortransgenes of any length and/or deletions of 1 base pair to over 1000 kb(or any value therebetween including, but not limited to, 1-100 basepairs, 1-50 base pairs, 1-30 base pairs, 1-20, 1-10, or 1-5 base pairs).

The modified cells of the invention may be a lymphoid cell (e.g., aT-cell), a stem/progenitor cell (e.g., an induced pluripotent stem cell(iPSC), an embryonic stem cell (e.g., human ES), a mesenchymal stem cell(MSC), or a hematopoietic stem cell (HSC). The stem cells may betotipotent or pluripotent (e.g., partially differentiated such as an HSCthat is a pluripotent myeloid or lymphoid stem cell). In otherembodiments, the invention provides methods for producing cells thathave a null phenotype for HLA expression. Any of the modified stem cellsdescribed herein (modified at the B2M locus) may then be differentiatedto generate a differentiated (in vivo or in vitro) cell descended from astem cell as described herein. Any of the modified stem cells describedherein may be comprise further modifications in other genes of interest(e.g. TCRA, TCRB, PD1, CTLA4 etc.).

In another aspect, the compositions (modified cells) and methodsdescribed herein can be used, for example, in the treatment orprevention or amelioration of a disorder. The methods typically comprise(a) cleaving or down regulating an endogenous B2M gene in an isolatedcell (e.g., T-cell or lymphocyte) using a nuclease (e.g., ZFN or TALEN)or nuclease system such as CRISPR/Cas or Cfp1/CRISPR with an engineeredcrRNA/tracr RNA, or using an engineered transcription factor (e.g.ZFN-TF, TALE-TF, Cfp1-TF or Cas9-TF) such that the B2M gene isinactivated or down modulated; and (b) introducing the cell into thesubject, thereby treating or preventing the disorder.

In some embodiments, a gene encoding TCR α (TCRA) and/or TCR β (TCRB) isalso inactivated or down modulated. In some embodiments inactivation isachieved via targeted cleavage of the constant region of this gene (TCRβ Constant region, or TRBC). In preferred embodiments, the gene encodingTCR α (TCRA) is inactivated or down modulated. In further preferredembodiments, the disorder is a cancer or an infectious disease. Infurther preferred embodiments inactivation is achieved via targetedcleavage of the constant region of this gene (TCR α Constant region,abbreviated TRAC).

The transcription factors and/or nuclease(s) can be introduced into acell as mRNA, in protein form and/or as a DNA sequence encoding thenuclease(s). In certain embodiments, the isolated cell introduced intothe subject further comprises additional genomic modification, forexample, an integrated exogenous sequence (into a cleaved B2M, TCR geneor other gene, for example a safe harbor gene or locus) and/orinactivation (e.g., nuclease-mediated) of additional genes, for exampleone or more HLA and/or TAP genes. The exogenous sequence may beintroduced via a vector (e.g. Ad, AAV, LV), or by using a technique suchas electroporation. In some embodiments, the proteins are introducedinto the cell by cell squeezing (see Kollmannsperger et al. (2016) NatComm 7:10372 doi:10.1038/ncomms10372). In some aspects, the compositionmay comprise isolated cell fragments and/or differentiated (partially orfully) cells.

In some aspects, the mature cells may be used for cell therapy, forexample, for adoptive cell transfer. In other embodiments, the cells foruse in T cell transplant contain another gene modification of interest.In one aspect, the T cells contain an inserted chimeric antigen receptor(CAR) specific for a cancer marker. In a further aspect, the insertedCAR is specific for the CD19 marker characteristic of B cellmalignancies. Such cells would be useful in a therapeutic compositionfor treating patients without having to match HLA, and so would be ableto be used as an “off-the-shelf” therapeutic for any patient in needthereof.

In another aspect, the B2M-modulated (modified) T cells contain aninserted Antibody-coupled T-cell Receptor (ACTR) donor sequence. In someembodiments, the ACTR donor sequence is inserted into a B2M or TCR geneto disrupt expression of that gene following nuclease-induced cleavage.In other embodiments, the donor sequence is inserted into a “safeharbor” locus, such as the AAVS1, HPRT, albumin and CCR5 genes. In someembodiments, the ACTR sequence is inserted via targeted integrationwhere the ACTR donor sequence comprises flanking homology arms that havehomology to the sequence flanking the cleavage site of the engineerednuclease. In some embodiments the ACTR donor sequence further comprisesa promoter and/or other transcriptional regulatory sequences. In otherembodiments, the ACTR donor sequence lacks a promoter. In someembodiments, the ACTR donor is inserted into a TCR β encoding gene(TCRB). In some embodiments insertion is achieved via targeted cleavageof the constant region of this gene (TCR β Constant region, or TRBC). Inpreferred embodiments, the ACTR donor is inserted into a TCR α encodinggene (TCRA). In further preferred embodiments insertion is achieved viatargeted cleavage of the constant region of this gene (TCR α Constantregion, abbreviated TRAC). In some embodiments, the donor is insertedinto an exon sequence in TCRA, while in others, the donor is insertedinto an intronic sequence in TCRA. In some embodiments, theTCR-modulated cells further comprise a CAR. In still furtherembodiments, the B2M-modulated cells are additionally modulated at anHLA gene or a checkpoint inhibitor gene.

Also provided are pharmaceutical compositions comprising the modifiedcells as described herein (e.g., T cells or stem cells with inactivatedB2M gene), or pharmaceutical compositions comprising one or more of theB2M-binding molecules (e.g., engineered transcription factors and/ornucleases) as described herein. In certain embodiments, thepharmaceutical compositions further comprise one or morepharmaceutically acceptable excipients. The modified cells, B2M-bindingmolecules (or polynucleotides encoding these molecules) and/orpharmaceutical compositions comprising these cells or molecules areintroduced into the subject via methods known in the art, e.g. throughintravenous infusion, infusion into a specific vessel such as thehepatic artery, or through direct tissue injection (e.g. muscle). Insome embodiments, the subject is an adult human with a disease orcondition that can be treated or ameliorated with the composition. Inother embodiments, the subject is a pediatric subject where thecomposition is administered to prevent, treat or ameliorate the diseaseor condition (e.g., cancer, graft versus host disease, etc.).

In some aspects, the composition (B2M modulated cells comprising anACTR) further comprises an exogenous antibody. See, also, U.S. PatentPublication No. 2017/0196992. In some aspects, the antibody is usefulfor arming an ACTR-comprising T cell to prevent or treat a condition. Insome embodiments, the antibody recognizes an antigen associated with atumor cell or with cancer associate processes such as EpCAM, CEA, gpA33,mucins, TAG-72, CAIX, PSMA, folate-binding antibodies, CD19, EGFR,ERBB2, ERBB3, MET, IGF1R, EPHA3, TRAILR1, TRAILR2, RANKL, FAP, VEGF,VEGFR, αVβ3 and α5β1 integrins, CD20, CD30, CD33, CD52, CTLA4, andenascin (Scott et al. (2012) Nat Rev Cancer 12:278). In otherembodiments, the antibody recognizes an antigen associated with aninfectious disease such as HIV, HCV and the like.

In another aspect, provided herein are B2M DNA-binding domains (e.g.,ZFPs, TALEs and sgRNAs) that bind to a target site in a B2M gene. Incertain embodiments, the DNA binding domain comprises a ZFP with therecognition helix regions in the order as shown in a single row of Table1; a TAL-effector domain DNA-binding protein with the RVDs as shown in asingle row of Table 2B; and/or a sgRNA as shown in a single row of Table2A. These DNA-binding proteins can be associated with transcriptionalregulatory domains to form engineered transcription factors thatmodulate B2M expression. Alternatively, these DNA-binding proteins canbe associated with one or more nuclease domains to form engineered zincfinger nucleases (ZFNs), TALENs and/or CRISPR/Cas systems that bind toand cleave a B2M gene. In certain embodiments, the ZFNs, TALENs orsingle guide RNAs (sgRNA) of a CRISPR/Cas system bind to target sites ina human B2M gene. The DNA-binding domain of the transcription factor ornuclease (e.g., ZFP, TALE, sgRNA) may bind to a target site in a B2Mgene comprising 9, 10, 11 12 or more (e.g., 13, 14, 15, 16, 17, 18, 19,20 or more) nucleotides of any of SEQ ID Nos: 6 to 48 or 137-205. Thezinc finger proteins may include 1, 2, 3, 4, 5, 6 or more zinc fingers,each zinc finger having a recognition helix that specifically contacts atarget subsite in the target gene. In certain embodiments, the zincfinger proteins comprise 4 or 5 or 6 fingers (designated F1, F2, F3, F4,F5 and F6 and ordered F1 to F4 or F5 or F6 from N-terminus toC-terminus), for example as shown in Table 1. In other embodiments, thesingle guide RNAs or TAL-effector DNA-binding domains may bind to atarget site shown in any of SEQ ID NOs:6-48 or 137-205 (or 12 or morebase pairs within any of SEQ ID Nos:6-48). Exemplary sgRNA target sitesare shown in SEQ ID NO:16-48 and exemplary TALEN binding sites are shownin Table 2B (SEQ ID Nos:137-205). Additional TALENs may be designed totarget sites as described herein using canonical or non-canonical RVDsas described in U.S. Pat. Nos. 8,586,526 and 9,458,205. The nucleasesdescribed herein (comprising a ZFP, a TALE or a sgRNA DNA-bindingdomain) are capable of making genetic modifications within a B2M genecomprising any of SEQ ID NO:6-48 or 137-205, including modifications(insertions and/or deletions) within any of these sequences (SEQ IDNO:6-48 or 137-205) and/or modifications to B2M gene sequences flankingthe target site sequences shown in SEQ ID NO:6-48 or 137-205, forinstance modifications within exon 1 or exon 2 of a B2M gene within oneor more of the following sequences: GGCCTTA, TCAAATT, TCAAAT, TTACTGAand/or AATTGAA.

Also provided are is fusion molecule comprising a DNA-binding domainthat binds to exon 1 or exon 2 of a B2M gene and a transcriptionalregulatory domain or a nuclease domain, wherein the DNA-binding domaincomprises a zinc finger protein (ZFP) as shown in a single row of Table1, a TALE-effector protein as shown in a single row of Table 2B or asingle guide RNA (sgRNA) as shown in a single row of Table 2A.

Any of the proteins described herein may further comprise a cleavagedomain and/or a cleavage half-domain (e.g., a wild-type or engineeredFokI cleavage half-domain). Thus, in any of the nucleases (e.g., ZFNs,TALENs, CRISPR/Cas systems) described herein, the nuclease domain maycomprise a wild-type nuclease domain or nuclease half-domain (e.g., aFokI cleavage half domain). In other embodiments, the nucleases (e.g.,ZFNs, TALENs, CRISPR/Cas nucleases) comprise engineered nuclease domainsor half-domains, for example engineered FokI cleavage half domains thatform obligate heterodimers. See, e.g., U.S. Patent Publication No.2008/0131962.

In another aspect, the disclosure provides a polynucleotide encoding anyof the proteins, fusion molecules and/or components thereof (e.g., sgRNAor other DNA-binding domain) described herein. The polynucleotide may bepart of a viral vector, a non-viral vector (e.g., plasmid) or be in mRNAform. Any of the polynucleotides described herein may also comprisesequences (donor, homology arms or patch sequences) for targetedinsertion into the B2M, TCR α and/or the TCR β gene. In yet anotheraspect, a gene delivery vector comprising any of the polynucleotidesdescribed herein is provided. In certain embodiments, the vector is anadenoviral vector (e.g., an Ad5/F35 vector) or a lentiviral vector (LV)including integration competent or integration-defective lentiviralvectors or an adeno-associated vector (AAV). Thus, also provided hereinare viral vectors comprising a sequence encoding a nuclease (e.g. ZFN orTALEN) and/or a nuclease system (CRISPR/Cas or Ttago) and/or a donorsequence for targeted integration into a target gene. In someembodiments, the donor sequence and the sequences encoding the nucleaseare on different vectors. In other embodiments, the nucleases aresupplied as polypeptides. In preferred embodiments, the polynucleotidesare mRNAs. In some aspects, the mRNA may be chemically modified (Seee.g. Kormann et al. (2011) Nature Biotechnology 29(2):154-157). In otheraspects, the mRNA may comprise an ARCA cap (see U.S. Pat. Nos. 7,074,596and 8,153,773). In some aspects, the mRNA may comprise a cap introducedby enzymatic modification. The enzymatically introduced cap may compriseCap0, Cap1 or Cap2 (see e.g. Smietanski et al. (2014) NatureCommunications 5:3004). In further aspects, the mRNA may be capped bychemical modification. In further embodiments, the mRNA may comprise amixture of unmodified and modified nucleotides (see U.S. PatentPublication No. 2012/0195936). In still further embodiments, the mRNAmay comprise a WPRE element (see U.S. Patent Publication No.2016/0326548). In some embodiments, the mRNA is double stranded (Seee.g. Kariko et al. (2011) Nucl Acid Res 39:e142).

In yet another aspect, the disclosure provides an isolated cellcomprising any of the proteins, polynucleotides and/or vectors describedherein. In certain embodiments, the cell is selected from the groupconsisting of a stem/progenitor cell, or a T-cell (e.g., CD4⁺ T-cell).In a still further aspect, the disclosure provides a cell or cell linewhich is descended from a cell or line comprising any of the proteins,polynucleotides and/or vectors described herein, namely a cell or cellline descended (e.g., in culture) from a cell in which B2M has beeninactivated by one or more ZFNs and/or in which a donor polynucleotide(e.g. ACTR, engineered TCR and/or CAR) has been stably integrated intothe genome of the cell. Thus, descendants of cells as described hereinmay not themselves comprise the proteins, polynucleotides and/or vectorsdescribed herein, but, in these cells, at least a B2M gene isinactivated and/or a donor polynucleotide is integrated into the genomeand/or expressed.

In another aspect, described herein are methods of inactivating a B2Mgene in a cell by introducing one or more proteins, polynucleotidesand/or vectors into the cell as described herein. In any of the methodsdescribed herein the nucleases may induce targeted mutagenesis,deletions of cellular DNA sequences, and/or facilitate targetedrecombination at a predetermined chromosomal locus. Thus, in certainembodiments, the nucleases delete or insert one or more nucleotides fromor into the target gene. In some embodiments the B2M gene is inactivatedby nuclease cleavage followed by non-homologous end joining. In otherembodiments, a genomic sequence in the target gene is replaced, forexample using a nuclease (or vector encoding said nuclease) as describedherein and a “donor” sequence that is inserted into the gene followingtargeted cleavage with the nuclease. The donor sequence may be presentin the nuclease vector, present in a separate vector (e.g., AAV, Ad orLV vector) or, alternatively, may be introduced into the cell using adifferent nucleic acid delivery mechanism.

Furthermore, any of the methods described herein can be practiced invitro, in vivo and/or ex vivo. In certain embodiments, the methods arepracticed ex vivo, for example to modify T-cells, to make them useful astherapeutics in an allogenic setting to treat a subject (e.g., a subjectwith cancer). Non-limiting examples of cancers that can be treatedand/or prevented include lung carcinomas, pancreatic cancers, livercancers, bone cancers, breast cancers, colorectal cancers, leukemias,ovarian cancers, lymphomas, brain cancers and the like.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a depiction the sequences of Exon1 and Exon 2 (SEQ ID NO: 1and 2) of the B2M gene targeted by the nucleases. Boxes indicate thefive different cleavage regions (A (GGCCTTA), C (TCAAATT), D (TCAAAT), E(TTACTGA) and G (AATTGAA)) that are flanked by the ZFN binding (target)sites.

FIG. 2A and FIG. 2B depict nuclease activity. FIG. 2A is a bar graphdepicting the percent of gene modification at each site in T cellstreated with ZFNs specific for B2M sites A, C, D, E and G as shown inFIG. 1 at a dose of either 2 or 6 μg. FIG. 2B depicts TALEN activityagainst the B2M gene in K562 cells.

FIG. 3 depicts the percent of HLA negative T cells following treatmentwith the B2M-specific ZFN pairs as analyzed by FACS analysis.

FIGS. 4A through 4E depict FACS results from treating cells with bothB2M and TCRA-specific ZFNs. FIG. 4A depicts the results for no ZFNtreatment, FIG. 4B shows the results following TCRA-specific ZFNs only(96% knock out of CD3 signal), and FIG. 4C shows the results followingB2M-specific ZFNs only (92% knock out of HLA signal). FIG. 4D is anillustration showing the location of cells that have a double knock out(resulting in a loss of both HLA marking and CD3 marking). FIG. 4E showsthe results following treatment of cells with both TCRA- andCD3-specific ZFNs, demonstrating a double knock out in 82% of the cells.

FIG. 5 shows results from TRAC (TCRA) and B2M double knockout andtargeted integration of a donor into either the TRAC (TCRA) or B2Mlocus.

DETAILED DESCRIPTION

Disclosed herein are compositions and methods for generating cells inwhich expression of a B2M gene is modulated such that the cells nolonger comprise a HLA class I on their cell surfaces. Cells modified inthis manner can be used as therapeutics, for example, transplants, asthe lack of B2M expression prevents or reduces an HLA-based immuneresponse. Additionally, other genes of interest may be inserted intocells in which the B2M gene has been manipulated and/or other genes ofinterest may be knocked out.

General

Practice of the methods, as well as preparation and use of thecompositions disclosed herein employ, unless otherwise indicated,conventional techniques in molecular biology, biochemistry, chromatinstructure and analysis, computational chemistry, cell culture,recombinant DNA and related fields as are within the skill of the art.These techniques are fully explained in the literature. See, forexample, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Secondedition, Cold Spring Harbor Laboratory Press, 1989 and Third edition,2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley& Sons, New York, 1987 and periodic updates; the series METHODS INENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE ANDFUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS INENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe,eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULARBIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) HumanaPress, Totowa, 1999.

Definitions

The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” areused interchangeably and refer to a deoxyribonucleotide orribonucleotide polymer, in linear or circular conformation, and ineither single- or double-stranded form. For the purposes of the presentdisclosure, these terms are not to be construed as limiting with respectto the length of a polymer. The terms can encompass known analogues ofnatural nucleotides, as well as nucleotides that are modified in thebase, sugar and/or phosphate moieties (e.g., phosphorothioatebackbones). In general, an analogue of a particular nucleotide has thesame base-pairing specificity; i.e., an analogue of A will base-pairwith T.

The terms “polypeptide,” “peptide” and “protein” are usedinterchangeably to refer to a polymer of amino acid residues. The termalso applies to amino acid polymers in which one or more amino acids arechemical analogues or modified derivatives of correspondingnaturally-occurring amino acids.

“Binding” refers to a sequence-specific, non-covalent interactionbetween macromolecules (e.g., between a protein and a nucleic acid). Notall components of a binding interaction need be sequence-specific (e.g.,contacts with phosphate residues in a DNA backbone), as long as theinteraction as a whole is sequence-specific. Such interactions aregenerally characterized by a dissociation constant (K_(d)) of 10⁻⁶ M⁻¹or lower. “Affinity” refers to the strength of binding: increasedbinding affinity being correlated with a lower K_(d). “Non-specificbinding” refers to, non-covalent interactions that occur between anymolecule of interest (e.g. an engineered nuclease) and a macromolecule(e.g. DNA) that are not dependent on target sequence.

A “DNA binding molecule” is a molecule that can bind to DNA. Such DNAbinding molecule can be a polypeptide, a domain of a protein, a domainwithin a larger protein or a polynucleotide. In some embodiments, thepolynucleotide is DNA, while in other embodiments, the polynucleotide isRNA. In some embodiments, the DNA binding molecule is a protein domainof a nuclease (e.g. the FokI domain), while in other embodiments, theDNA binding molecule is a guide RNA component of an RNA-guided nuclease(e.g. Cas9 or Cfp1).

A “binding protein” is a protein that is able to bind non-covalently toanother molecule. A binding protein can bind to, for example, a DNAmolecule (a DNA-binding protein), an RNA molecule (an RNA-bindingprotein) and/or a protein molecule (a protein-binding protein). In thecase of a protein-binding protein, it can bind to itself (to formhomodimers, homotrimers, etc.) and/or it can bind to one or moremolecules of a different protein or proteins. A binding protein can havemore than one type of binding activity. For example, zinc fingerproteins have DNA-binding, RNA-binding and protein-binding activity.

A “zinc finger DNA binding protein” (or binding domain) is a protein, ora domain within a larger protein, that binds DNA in a sequence-specificmanner through one or more zinc fingers, which are regions of amino acidsequence within the binding domain whose structure is stabilized throughcoordination of a zinc ion. The term zinc finger DNA binding protein isoften abbreviated as zinc finger protein or ZFP.

A “TALE DNA binding domain” or “TALE” is a polypeptide comprising one ormore TALE repeat domains/units. The repeat domains, each comprising arepeat variable diresidue (RVD), are involved in binding of the TALE toits cognate target DNA sequence. A single “repeat unit” (also referredto as a “repeat”) is typically 33-35 amino acids in length and exhibitsat least some sequence homology with other TALE repeat sequences withina naturally occurring TALE protein. TALE proteins may be designed tobind to a target site using canonical or non-canonical RVDs within therepeat units. See, e.g., U.S. Pat. Nos. 8,586,526 and 9,458,205,incorporated by reference herein in its entirety.

Zinc finger and TALE DNA-binding domains can be “engineered” to bind toa predetermined nucleotide sequence, for example via engineering(altering one or more amino acids) of the recognition helix region of anaturally occurring zinc finger protein or by engineering of the aminoacids involved in DNA binding (the repeat variable diresidue or RVDregion). Therefore, engineered zinc finger proteins or TALE proteins areproteins that are non-naturally occurring. Non-limiting examples ofmethods for engineering zinc finger proteins and TALEs are design andselection. A designed protein is a protein not occurring in nature whosedesign/composition results principally from rational criteria. Rationalcriteria for design include application of substitution rules andcomputerized algorithms for processing information in a database storinginformation of existing ZFP or TALE designs (canonical and non-canonicalRVDs) and binding data. See, for example, U.S. Pat. Nos. 9,458,205;8,586,526; 6,140,081; 6,453,242; and 6,534,261; see also InternationalPatent Publication Nos. WO 98/53058; WO 98/53059; WO 98/53060; WO02/016536; and WO 03/016496.

A “selected” zinc finger protein, TALE protein or CRISPR/Cas system isnot found in nature and whose production results primarily from anempirical process such as phage display, interaction trap or hybridselection. See e.g., U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988;6,013,453; and 6,200,759; International Patent Publication Nos. WO95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO01/60970; WO 01/88197; and WO 02/099084.

“TtAgo” is a prokaryotic Argonaute protein thought to be involved ingene silencing. TtAgo is derived from the bacteria Thermus thermophilus.See, e.g. Swarts et al., ibid, G. Sheng et al. (2014) Proc. Natl. Acad.Sci. U.S.A. 111:652). A “TtAgo system” is all the components requiredincluding e.g. guide DNAs for cleavage by a TtAgo enzyme.

“Recombination” refers to a process of exchange of genetic informationbetween two polynucleotides. For the purposes of this disclosure,“homologous recombination (HR)” refers to the specialized form of suchexchange that takes place, for example, during repair of double-strandbreaks in cells via homology-directed repair mechanisms. This processrequires nucleotide sequence homology, uses a “donor” molecule totemplate repair of a “target” molecule (i.e., the one that experiencedthe double-strand break), and is variously known as “non-crossover geneconversion” or “short tract gene conversion,” because it leads to thetransfer of genetic information from the donor to the target. Withoutwishing to be bound by any particular theory, such transfer can involvemismatch correction of heteroduplex DNA that forms between the brokentarget and the donor, and/or “synthesis-dependent strand annealing,” inwhich the donor is used to resynthesize genetic information that willbecome part of the target, and/or related processes. Such specialized HRoften results in an alteration of the sequence of the target moleculesuch that part or all of the sequence of the donor polynucleotide isincorporated into the target polynucleotide.

In the methods of the disclosure, one or more targeted nucleases asdescribed herein create a double-stranded break (DSB) in the targetsequence (e.g., cellular chromatin) at a predetermined site (e.g. a geneor locus of interest), and a “donor” polynucleotide, having homology tothe nucleotide sequence in the region of the break, can be introducedinto the cell. The presence of the DSB has been shown to facilitateintegration of the donor sequence. Optionally, the construct hashomology to the nucleotide sequence in the region of the break. Thedonor sequence may be physically integrated or, alternatively, the donorpolynucleotide is used as a template for repair of the break viahomologous recombination, resulting in the introduction of all or partof the nucleotide sequence as in the donor into the cellular chromatin.Thus, a first sequence in cellular chromatin can be altered and, incertain embodiments, can be converted into a sequence present in a donorpolynucleotide. Thus, the use of the terms “replace” or “replacement”can be understood to represent replacement of one nucleotide sequence byanother, (i.e., replacement of a sequence in the informational sense),and does not necessarily require physical or chemical replacement of onepolynucleotide by another.

In any of the methods described herein, additional pairs of zinc-fingerproteins can be used for additional double-stranded cleavage ofadditional target sites within the cell.

In certain embodiments of methods for targeted recombination and/orreplacement and/or alteration of a sequence in a region of interest incellular chromatin, a chromosomal sequence is altered by homologousrecombination with an exogenous “donor” nucleotide sequence. Suchhomologous recombination is stimulated by the presence of adouble-stranded break in cellular chromatin, if sequences homologous tothe region of the break are present.

In any of the methods described herein, the first nucleotide sequence(the “donor sequence”) can contain sequences that are homologous, butnot identical, to genomic sequences in the region of interest, therebystimulating homologous recombination to insert a non-identical sequencein the region of interest. Thus, in certain embodiments, portions of thedonor sequence that are homologous to sequences in the region ofinterest exhibit between about 80 to 99% (or any integer therebetween)sequence identity to the genomic sequence that is replaced. In otherembodiments, the homology between the donor and genomic sequence ishigher than 99%, for example if only 1 nucleotide differs as betweendonor and genomic sequences of over 100 contiguous base pairs. Incertain cases, a non-homologous portion of the donor sequence cancontain sequences not present in the region of interest, such that newsequences are introduced into the region of interest. In theseinstances, the non-homologous sequence is generally flanked by sequencesof 50-1,000 base pairs (or any integral value therebetween) or anynumber of base pairs greater than 1,000, that are homologous oridentical to sequences in the region of interest. In other embodiments,the donor sequence is non-homologous to the first sequence, and isinserted into the genome by non-homologous recombination mechanisms.

Any of the methods described herein can be used for partial or completeinactivation of one or more target sequences in a cell by targetedintegration of donor sequence that disrupts expression of the gene(s) ofinterest. Cell lines with partially or completely inactivated genes arealso provided.

Furthermore, the methods of targeted integration as described herein canalso be used to integrate one or more exogenous sequences. The exogenousnucleic acid sequence can comprise, for example, one or more genes orcDNA molecules, or any type of coding or noncoding sequence, as well asone or more control elements (e.g., promoters). In addition, theexogenous nucleic acid sequence may produce one or more RNA molecules(e.g., small hairpin RNAs (shRNAs), inhibitory RNAs (RNAis), microRNAs(miRNAs), etc.).

“Cleavage” refers to the breakage of the covalent backbone of a DNAmolecule. Cleavage can be initiated by a variety of methods including,but not limited to, enzymatic or chemical hydrolysis of a phosphodiesterbond. Both single-stranded cleavage and double-stranded cleavage arepossible, and double-stranded cleavage can occur as a result of twodistinct single-stranded cleavage events. DNA cleavage can result in theproduction of either blunt ends or staggered ends. In certainembodiments, fusion polypeptides are used for targeted double-strandedDNA cleavage.

A “cleavage half-domain” is a polypeptide sequence which, in conjunctionwith a second polypeptide (either identical or different) forms acomplex having cleavage activity (preferably double-strand cleavageactivity). The terms “first and second cleavage half-domains;” “+ and−cleavage half-domains” and “right and left cleavage half-domains” areused interchangeably to refer to pairs of cleavage half-domains thatdimerize.

An “engineered cleavage half-domain” is a cleavage half-domain that hasbeen modified so as to form obligate heterodimers with another cleavagehalf-domain (e.g., another engineered cleavage half-domain). See, also,U.S. Pat. Nos. 7,888,121; 7,914,796; 8,034,598; 8,623,618 and U.S.Patent Publication No. 2011/0201055, incorporated herein by reference intheir entireties.

The term “sequence” refers to a nucleotide sequence of any length, whichcan be DNA or RNA; can be linear, circular or branched and can be eithersingle-stranded or double stranded. The term “donor sequence” refers toa nucleotide sequence that is inserted into a genome. A donor sequencecan be of any length, for example between 2 and 10,000 nucleotides inlength (or any integer value therebetween or thereabove), preferablybetween about 100 and 1,000 nucleotides in length (or any integertherebetween), more preferably between about 200 and 500 nucleotides inlength.

“Chromatin” is the nucleoprotein structure comprising the cellulargenome. Cellular chromatin comprises nucleic acid, primarily DNA, andprotein, including histones and non-histone chromosomal proteins. Themajority of eukaryotic cellular chromatin exists in the form ofnucleosomes, wherein a nucleosome core comprises approximately 150 basepairs of DNA associated with an octamer comprising two each of histonesH2A, H2B, H3 and H4; and linker DNA (of variable length depending on theorganism) extends between nucleosome cores. A molecule of histone H1 isgenerally associated with the linker DNA. For the purposes of thepresent disclosure, the term “chromatin” is meant to encompass all typesof cellular nucleoprotein, both prokaryotic and eukaryotic. Cellularchromatin includes both chromosomal and episomal chromatin.

A “chromosome” is a chromatin complex comprising all or a portion of thegenome of a cell. The genome of a cell is often characterized by itskaryotype, which is the collection of all the chromosomes that comprisethe genome of the cell. The genome of a cell can comprise one or morechromosomes.

An “episome” is a replicating nucleic acid, nucleoprotein complex orother structure comprising a nucleic acid that is not part of thechromosomal karyotype of a cell. Examples of episomes include plasmidsand certain viral genomes.

A “target site” or “target sequence” is a nucleic acid sequence thatdefines a portion of a nucleic acid to which a binding molecule willbind, provided sufficient conditions for binding exist. For example, thesequence 5′ GAATTC 3′ is a target site for the Eco RI restrictionendonuclease.

An “exogenous” molecule is a molecule that is not normally present in acell, but can be introduced into a cell by one or more genetic,biochemical or other methods. “Normal presence in the cell” isdetermined with respect to the particular developmental stage andenvironmental conditions of the cell. Thus, for example, a molecule thatis present only during embryonic development of muscle is an exogenousmolecule with respect to an adult muscle cell. Similarly, a moleculeinduced by heat shock is an exogenous molecule with respect to anon-heat-shocked cell. An exogenous molecule can comprise, for example,a functioning version of a malfunctioning endogenous molecule or amalfunctioning version of a normally-functioning endogenous molecule.

An exogenous molecule can be, among other things, a small molecule, suchas is generated by a combinatorial chemistry process, or a macromoleculesuch as a protein, nucleic acid, carbohydrate, lipid, glycoprotein,lipoprotein, polysaccharide, any modified derivative of the abovemolecules, or any complex comprising one or more of the above molecules.Nucleic acids include DNA and RNA, can be single- or double-stranded;can be linear, branched or circular; and can be of any length. See,e.g., U.S. Pat. Nos. 8,703,489 and 9,255,259. Nucleic acids includethose capable of forming duplexes, as well as triplex-forming nucleicacids. See, for example, U.S. Pat. Nos. 5,176,996 and 5,422,251.Proteins include, but are not limited to, DNA-binding proteins,transcription factors, chromatin remodeling factors, methylated DNAbinding proteins, polymerases, methylases, demethylases, acetylases,deacetylases, kinases, phosphatases, integrases, recombinases, ligases,topoisomerases, gyrases and helicases.

An exogenous molecule can be the same type of molecule as an endogenousmolecule, e.g., an exogenous protein or nucleic acid. For example, anexogenous nucleic acid can comprise an infecting viral genome, a plasmidor episome introduced into a cell, or a chromosome that is not normallypresent in the cell. Methods for the introduction of exogenous moleculesinto cells are known to those of skill in the art and include, but arenot limited to, lipid-mediated transfer (i.e., liposomes, includingneutral and cationic lipids), electroporation, direct injection, cellfusion, particle bombardment, calcium phosphate co-precipitation,DEAE-dextran-mediated transfer and viral vector-mediated transfer. Anexogenous molecule can also be the same type of molecule as anendogenous molecule but derived from a different species than the cellis derived from. For example, a human nucleic acid sequence may beintroduced into a cell line originally derived from a mouse or hamster.

By contrast, an “endogenous” molecule is one that is normally present ina particular cell at a particular developmental stage under particularenvironmental conditions. For example, an endogenous nucleic acid cancomprise a chromosome, the genome of a mitochondrion, chloroplast orother organelle, or a naturally-occurring episomal nucleic acid.Additional endogenous molecules can include proteins, for example,transcription factors and enzymes.

A “fusion” molecule is a molecule in which two or more subunit moleculesare linked, preferably covalently. The subunit molecules can be the samechemical type of molecule, or can be different chemical types ofmolecules. Examples of the first type of fusion molecule include, butare not limited to, fusion proteins (for example, a fusion between a ZFPor TALE DNA-binding domain and one or more activation domains) andfusion nucleic acids (for example, a nucleic acid encoding the fusionprotein described supra). Examples of the second type of fusion moleculeinclude, but are not limited to, a fusion between a triplex-formingnucleic acid and a polypeptide, and a fusion between a minor groovebinder and a nucleic acid. The term also includes systems in which apolynucleotide component associates with a polypeptide component to forma functional molecule (e.g., a CRISPR/Cas system in which a single guideRNA associates with a functional domain to modulate gene expression).

Expression of a fusion protein in a cell can result from delivery of thefusion protein to the cell or by delivery of a polynucleotide encodingthe fusion protein to a cell, wherein the polynucleotide is transcribed,and the transcript is translated, to generate the fusion protein.Trans-splicing, polypeptide cleavage and polypeptide ligation can alsobe involved in expression of a protein in a cell. Methods forpolynucleotide and polypeptide delivery to cells are presented elsewherein this disclosure.

A “gene” for the purposes of the present disclosure, includes a DNAregion encoding a gene product (see infra), as well as all DNA regionswhich regulate the production of the gene product, whether or not suchregulatory sequences are adjacent to coding and/or transcribedsequences. Accordingly, a gene includes, but is not necessarily limitedto, promoter sequences, terminators, translational regulatory sequencessuch as ribosome binding sites and internal ribosome entry sites,enhancers, silencers, insulators, boundary elements, replicationorigins, matrix attachment sites and locus control regions.

A “safe harbor” locus is a locus within the genome wherein a gene may beinserted without any deleterious effects on the host cell. Mostbeneficial is a safe harbor locus in which expression of the insertedgene sequence is not perturbed by any read-through expression fromneighboring genes. Non-limiting examples of safe harbor loci that aretargeted by nuclease(s) include CCR5, CCR5, HPRT, AAVS1, Rosa andalbumin. See, e.g., U.S. Pat. Nos. 8,771,985; 8,110,379; 7,951,925; U.S.Patent Publication Nos. 2010/0218264; 2011/0265198; 2013/0137104;2013/0122591; 2013/0177983; 2013/0177960; 2015/0056705 and2015/0159172).

“Gene expression” refers to the conversion of the information, containedin a gene, into a gene product. A gene product can be the directtranscriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisenseRNA, ribozyme, structural RNA or any other type of RNA) or a proteinproduced by translation of an mRNA. Gene products also include RNAswhich are modified, by processes such as capping, polyadenylation,methylation, and editing, and proteins modified by, for example,methylation, acetylation, phosphorylation, ubiquitination,ADP-ribosylation, myristilation, and glycosylation.

“Modulation” or “modification” of gene expression refers to a change inthe activity of a gene. Modulation of expression can include, but is notlimited to, gene activation and gene repression, including bymodification of the gene via binding of an exogenous molecule (e.g.,engineered transcription factor). Modulation may also be achieved bymodification of the gene sequence via genome editing (e.g., cleavage,alteration, inactivation, random mutation). Gene inactivation refers toany reduction in gene expression as compared to a cell that has not beenmodified as described herein. Thus, gene inactivation may be partial orcomplete.

A “region of interest” is any region of cellular chromatin, such as, forexample, a gene or a non-coding sequence within or adjacent to a gene,in which it is desirable to bind an exogenous molecule. Binding can befor the purposes of targeted DNA cleavage and/or targeted recombination.A region of interest can be present in a chromosome, an episome, anorganellar genome (e.g., mitochondrial, chloroplast), or an infectingviral genome, for example. A region of interest can be within the codingregion of a gene, within transcribed non-coding regions such as, forexample, leader sequences, trailer sequences or introns, or withinnon-transcribed regions, either upstream or downstream of the codingregion. A region of interest can be as small as a single nucleotide pairor up to 2,000 nucleotide pairs in length, or any integral value ofnucleotide pairs.

“Eukaryotic” cells include, but are not limited to, fungal cells (suchas yeast), plant cells, animal cells, mammalian cells and human cells(e.g., T-cells).

The terms “operative linkage” and “operatively linked” (or “operablylinked”) are used interchangeably with reference to a juxtaposition oftwo or more components (such as sequence elements), in which thecomponents are arranged such that both components function normally andallow the possibility that at least one of the components can mediate afunction that is exerted upon at least one of the other components. Byway of illustration, a transcriptional regulatory sequence, such as apromoter, is operatively linked to a coding sequence if thetranscriptional regulatory sequence controls the level of transcriptionof the coding sequence in response to the presence or absence of one ormore transcriptional regulatory factors. A transcriptional regulatorysequence is generally operatively linked in cis with a coding sequence,but need not be directly adjacent to it. For example, an enhancer is atranscriptional regulatory sequence that is operatively linked to acoding sequence, even though they are not contiguous.

With respect to fusion polypeptides, the term “operatively linked” canrefer to the fact that each of the components performs the same functionin linkage to the other component as it would if it were not so linked.For example, with respect to a fusion polypeptide in which a DNA-bindingdomain (e.g., ZFP, TALE) is fused to an activation domain, theDNA-binding domain and the activation domain are in operative linkageif, in the fusion polypeptide, the DNA-binding domain portion is able tobind its target site and/or its binding site, while the activationdomain is able to up-regulate gene expression. When a fusion polypeptidein which a DNA-binding domain is fused to a cleavage domain, theDNA-binding domain and the cleavage domain are in operative linkage if,in the fusion polypeptide, the DNA-binding domain portion is able tobind its target site and/or its binding site, while the cleavage domainis able to cleave DNA in the vicinity of the target site. Similarly,with respect to a fusion polypeptide in which a DNA-binding domain isfused to an activation or repression domain, the DNA-binding domain andthe activation or repression domain are in operative linkage if, in thefusion polypeptide, the DNA-binding domain portion is able to bind itstarget site and/or its binding site, while the activation domain is ableto upregulate gene expression or the repression domain is able todownregulate gene expression.

A “functional fragment” of a protein, polypeptide or nucleic acid is aprotein, polypeptide or nucleic acid whose sequence is not identical tothe full-length protein, polypeptide or nucleic acid, yet retains thesame function as the full-length protein, polypeptide or nucleic acid. Afunctional fragment can possess more, fewer, or the same number ofresidues as the corresponding native molecule, and/or can contain one ormore amino acid or nucleotide substitutions. Methods for determining thefunction of a nucleic acid (e.g., coding function, ability to hybridizeto another nucleic acid) are well-known in the art. Similarly, methodsfor determining protein function are well-known. For example, theDNA-binding function of a polypeptide can be determined, for example, byfilter-binding, electrophoretic mobility-shift, or immunoprecipitationassays. DNA cleavage can be assayed by gel electrophoresis. See Ausubelet al., supra. The ability of a protein to interact with another proteincan be determined, for example, by co-immunoprecipitation, two-hybridassays or complementation, both genetic and biochemical. See, forexample, Fields et al. (1989) Nature 340:245-246; U.S. Pat. No.5,585,245 and International Patent Publication No. WO 98/44350.

A “vector” is capable of transferring gene sequences to target cells.Typically, “vector construct,” “expression vector,” “expressionconstruct,” “expression cassette,’ and “gene transfer vector,” mean anynucleic acid construct capable of directing the expression of a gene ofinterest and which can transfer gene sequences to target cells. Thus,the term includes cloning, and expression vehicles, as well asintegrating vectors.

A “reporter gene” or “reporter sequence” refers to any sequence thatproduces a protein product that is easily measured, preferably althoughnot necessarily in a routine assay. Suitable reporter genes include, butare not limited to, sequences encoding proteins that mediate antibioticresistance (e.g., ampicillin resistance, neomycin resistance, G418resistance, puromycin resistance), sequences encoding colored orfluorescent or luminescent proteins (e.g., green fluorescent protein,enhanced green fluorescent protein, red fluorescent protein,luciferase), and proteins which mediate enhanced cell growth and/or geneamplification (e.g., dihydrofolate reductase). Epitope tags include, forexample, one or more copies of FLAG, His, myc, Tap, HA or any detectableamino acid sequence. “Expression tags” include sequences that encodereporters that may be operably linked to a desired gene sequence inorder to monitor expression of the gene of interest.

The terms “subject” and “patient” are used interchangeably and refer tomammals such as human patients and non-human primates, as well asexperimental animals such as rabbits, dogs, cats, rats, mice, and otheranimals. Accordingly, the term “subject” or “patient” as used hereinmeans any mammalian patient or subject to which the expression cassettesof the invention can be administered. Subjects of the present inventioninclude those with a disorder or those at risk for developing adisorder.

The terms “treating” and “treatment” as used herein refer to reductionin severity and/or frequency of symptoms, elimination of symptoms and/orunderlying cause, prevention of the occurrence of symptoms and/or theirunderlying cause, and improvement or remediation of damage. Cancer andgraft versus host disease are non-limiting examples of conditions thatmay be treated using the compositions and methods described herein.Thus, “treating” and “treatment includes:

(i) preventing the disease or condition from occurring in a mammal, inparticular, when such mammal is predisposed to the condition but has notyet been diagnosed as having it;

(ii) inhibiting the disease or condition, i.e., arresting itsdevelopment;

(iii) relieving the disease or condition, i.e., causing regression ofthe disease or condition; or

(iv) relieving the symptoms resulting from the disease or condition,i.e., relieving pain without addressing the underlying disease orcondition.

As used herein, the terms “disease” and “condition” may be usedinterchangeably or may be different in that the particular malady orcondition may not have a known causative agent (so that etiology has notyet been worked out) and it is therefore not yet recognized as a diseasebut only as an undesirable condition or syndrome, wherein a more or lessspecific set of symptoms have been identified by clinicians.

A “pharmaceutical composition” refers to a formulation of a compound ofthe invention and a medium generally accepted in the art for thedelivery of the biologically active compound to mammals, e.g., humans.Such a medium includes all pharmaceutically acceptable carriers,diluents or excipients therefor.

“Effective amount” or “therapeutically effective amount” refers to thatamount of a compound of the invention which, when administered to amammal, preferably a human, is sufficient to effect treatment in themammal, preferably a human. The amount of a composition of the inventionwhich constitutes a “therapeutically effective amount” will varydepending on the compound, the condition and its severity, the manner ofadministration, and the age of the mammal to be treated, but can bedetermined routinely by one of ordinary skill in the art having regardto his own knowledge and to this disclosure.

DNA-Binding Domains

Described herein are compositions comprising a DNA-binding domain thatspecifically binds to a target site in any gene comprising a HLA gene ora HLA regulator, including a B2M gene. Any DNA-binding domain can beused in the compositions and methods disclosed herein, including but notlimited to a zinc finger DNA-binding domain, a TALE DNA binding domain,the DNA-binding portion (sgRNA) of a CRISPR/Cas nuclease, or aDNA-binding domain from a meganuclease. The DNA-binding domain may bindto any target sequence within the gene, including, but not limited to, atarget sequence of 12 or more nucleotides as shown in any of SEQ IDNO:6-48.

In certain embodiments, the DNA binding domain comprises a zinc fingerprotein. Preferably, the zinc finger protein is non-naturally occurringin that it is engineered to bind to a target site of choice. See, forexample, Beerli et al. (2002) Nature Biotechnol. 20:135-141; Pabo et al.(2001) Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001) NatureBiotechnol. 19:656-660; Segal et al. (2001) Curr. Opin. Biotechnol.12:632-637; Choo et al. (2000) Curr. Opin. Struct. Biol. 10:411-416;U.S. Pat. Nos. 6,453,242; 6,534,261; 6,599,692; 6,503,717; 6,689,558;7,030,215; 6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; and7,253,273; and U.S. Patent Publication Nos. 2005/0064474; 2007/0218528;2005/0267061, all incorporated herein by reference in their entireties.In certain embodiments, the DNA-binding domain comprises a zinc fingerprotein disclosed in U.S. Patent Publication No. 2012/0060230 (e.g.,Table 1), incorporated by reference in its entirety herein.

An engineered zinc finger binding domain can have a novel bindingspecificity, compared to a naturally-occurring zinc finger protein.Engineering methods include, but are not limited to, rational design andvarious types of selection. Rational design includes, for example, usingdatabases comprising triplet (or quadruplet) nucleotide sequences andindividual zinc finger amino acid sequences, in which each triplet orquadruplet nucleotide sequence is associated with one or more amino acidsequences of zinc fingers which bind the particular triplet orquadruplet sequence. See, for example, U.S. Pat. Nos. 6,453,242 and6,534,261, incorporated by reference herein in their entireties.

Exemplary selection methods, including phage display and two-hybridsystems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523;6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; aswell as International Patent Publication Nos. WO 98/37186; WO 98/53057;WO 00/27878; and WO 01/88197 and GB 2,338,237. In addition, enhancementof binding specificity for zinc finger binding domains has beendescribed, for example, in U.S. Pat. No. 6,794,136.

In addition, as disclosed in these and other references, zinc fingerdomains and/or multi-fingered zinc finger proteins may be linkedtogether using any suitable linker sequences, including for example,linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos.6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 ormore amino acids in length. The proteins described herein may includeany combination of suitable linkers between the individual zinc fingersof the protein. In addition, enhancement of binding specificity for zincfinger binding domains has been described, for example, in U.S. Pat. No.6,794,136.

Selection of target sites; ZFPs and methods for design and constructionof fusion proteins (and polynucleotides encoding same) are known tothose of skill in the art and described in detail in U.S. Pat. Nos.6,140,081; 5,789,538; 6,453,242; 6,534,261; 5,925,523; 6,007,988;6,013,453; and 6,200,759 and International Patent Publication Nos. WO95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO01/60970; WO 01/88197; WO 02/099084; WO 98/53058; WO 98/53059; WO98/53060; WO 02/016536; and WO 03/016496.

In addition, as disclosed in these and other references, zinc fingerdomains and/or multi-fingered zinc finger proteins may be linkedtogether using any suitable linker sequences, including for example,linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos.6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 ormore amino acids in length. The proteins described herein may includeany combination of suitable linkers between the individual zinc fingersof the protein.

In certain embodiments, the DNA binding domain is an engineered zincfinger protein that binds (in a sequence-specific manner) to a targetsite in a B2M gene or B2M regulatory gene and modulates expression of aB2M gene. In some embodiments, the zinc finger protein binds to a targetsite in B2M, while in other embodiments, the zinc finger binds to atarget site in B2M.

Usually, the ZFPs include at least three fingers. Certain of the ZFPsinclude four, five or six fingers. The ZFPs that include three fingerstypically recognize a target site that includes 9 or 10 nucleotides;ZFPs that include four fingers typically recognize a target site thatincludes 12 to 14 nucleotides; while ZFPs having six fingers canrecognize target sites that include 18 to 21 nucleotides. The ZFPs canalso be fusion proteins that include one or more regulatory domains,which domains can be transcriptional activation or repression domains.

In some embodiments, the DNA-binding domain may be derived from anuclease. For example, the recognition sequences of homing endonucleasesand meganucleases such as I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV,I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII andI-TevIII are known. See also U.S. Pat. Nos. 5,420,032; 6,833,252;Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al.(1989) Gene 82:115118; Perler et al. (1994) Nucleic Acids Res. 22:1125-1127; Jasin (1996) Trends Genet. 12:224228; Gimble et al. (1996) J.Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353and the New England Biolabs catalogue. In addition, the DNA-bindingspecificity of homing endonucleases and meganucleases can be engineeredto bind non-natural target sites. See, for example, Chevalier et al.(2002) Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic Acids Res.31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques et al.(2007) Current Gene Therapy 7:49-66; U.S. Patent Publication No.2007/0117128.

In other embodiments, the DNA binding domain comprises an engineereddomain from a TAL effector similar to those derived from the plantpathogens Xanthomonas (see Boch et al. (2009) Science 326:1509-1512 andMoscou and Bogdanove (2009) Science 326:1501) and Ralstonia (see Heueret al. (2007) Applied and Environmental Microbiology 73(13):4379-4384);U.S. Patent Publication Nos. 2011/0301073 and 2011/0145940. The plantpathogenic bacteria of the genus Xanthomonas are known to cause manydiseases in important crop plants. Pathogenicity of Xanthomonas dependson a conserved type III secretion (T3S) system which injects more than25 different effector proteins into the plant cell. Among these injectedproteins are transcription activator-like effectors (TALE) which mimicplant transcriptional activators and manipulate the plant transcriptome(see Kay et al. (2007) Science 318:648-651). These proteins contain aDNA binding domain and a transcriptional activation domain. One of themost well characterized TALEs is AvrBs3 from Xanthomonas campestgris pv.Vesicatoria (see Bonas et al. (1989) Mol Gen Genet 218:127-136 andInternational Patent Publication No. WO 2010/079430). TALEs contain acentralized domain of tandem repeats, each repeat containingapproximately 34 amino acids, which are key to the DNA bindingspecificity of these proteins. In addition, they contain a nuclearlocalization sequence and an acidic transcriptional activation domain(for a review see Schornack S., et al. (2006) J Plant Physiol163(3):256-272). In addition, in the phytopathogenic bacteria Ralstoniasolanacearum two genes, designated brg11 and hpx17 have been found thatare homologous to the AvrBs3 family of Xanthomonas in the R.solanacearum biovar 1 strain GMI1000 and in the biovar 4 strain RS1000(See Heuer et al. (2007) Appl and Envir Micro 73(13):4379-4384). Thesegenes are 98.9% identical in nucleotide sequence to each other butdiffer by a deletion of 1,575 bp in the repeat domain of hpx17. However,both gene products have less than 40% sequence identity with AvrBs3family proteins of Xanthomonas.

Specificity of these TAL effectors depends on the sequences found in thetandem repeats. The repeated sequence comprises approximately 102 basepairs and the repeats are typically 91-100% homologous with each other(Bonas et al., ibid). Polymorphism of the repeats is usually located atpositions 12 and 13 and there appears to be a one-to-one correspondencebetween the identity of the hypervariable diresidues (the repeatvariable diresidue or RVD region) at positions 12 and 13 with theidentity of the contiguous nucleotides in the TAL-effector's targetsequence (see Moscou and Bogdanove (2009) Science 326:1501 and Boch etal. (2009) Science 326:1509-1512). Experimentally, the natural code forDNA recognition of these TAL-effectors has been determined such that anHD sequence at positions 12 and 13 (Repeat Variable Diresidue or RVD)leads to a binding to cytosine (C), NG binds to T, NI to A, C, G or T,NN binds to A or G, and ING binds to T. These DNA binding repeats havebeen assembled into proteins with new combinations and numbers ofrepeats, to make artificial transcription factors that are able tointeract with new sequences and activate the expression of anon-endogenous reporter gene in plant cells (Boch et al., ibid).Engineered TAL proteins have been linked to a FokI cleavage half domainto yield a TAL effector domain nuclease fusion (TALEN), including TALENswith atypical RVDs. See, e.g., U.S. Pat. No. 8,586,526.

In some embodiments, the TALEN comprises an endonuclease (e.g., FokI)cleavage domain or cleavage half-domain. In other embodiments, theTALE-nuclease is a mega TAL. These mega TAL nucleases are fusionproteins comprising a TALE DNA binding domain and a meganucleasecleavage domain. The meganuclease cleavage domain is active as a monomerand does not require dimerization for activity. (See Boissel et al.(2013) Nucl Acid Res 42:4:2591-2601, doi: 10.1093/nar/gkt1224).

In still further embodiments, the nuclease comprises a compact TALEN.These are single chain fusion proteins linking a TALE DNA binding domainto a TevI nuclease domain. The fusion protein can act as either anickase localized by the TALE region, or can create a double strandbreak, depending upon where the TALE DNA binding domain is located withrespect to the TevI nuclease domain (see Beurdeley et al. (2013) NatComm 1-8 DOI: 10.1038/ncomms2782). In addition, the nuclease domain mayalso exhibit DNA-binding functionality. Any TALENs may be used incombination with additional TALENs (e.g., one or more TALENs (cTALENs orFokI-TALENs) with one or more mega-TALEs.

In addition, as disclosed in these and other references, zinc fingerdomains and/or multi-fingered zinc finger proteins or TALEs may belinked together using any suitable linker sequences, including forexample, linkers of 5 or more amino acids in length. See, also, U.S.Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linkersequences 6 or more amino acids in length. The proteins described hereinmay include any combination of suitable linkers between the individualzinc fingers of the protein. In addition, enhancement of bindingspecificity for zinc finger binding domains has been described, forexample, in U.S. Pat. No. 6,794,136.

In certain embodiments, the DNA-binding domain is part of a CRISPR/Casnuclease system, including a single guide RNA (sgRNA) that binds to DNA.See, e.g., U.S. Pat. No. 8,697,359 and U.S. Patent Publication Nos.2015/0056705 and 2015/0159172. The CRISPR (clustered regularlyinterspaced short palindromic repeats) locus, which encodes RNAcomponents of the system, and the cas (CRISPR-associated) locus, whichencodes proteins (Jansen et al. (2002) Mol. Microbiol. 43:1565-1575;Makarova et al. (2002) Nucleic Acids Res. 30:482-496; Makarova et al.(2006) Biol. Direct 1:7; Haft et al. (2005) PLoS Comput. Biol. 1:e60)make up the gene sequences of the CRISPR/Cas nuclease system. CRISPRloci in microbial hosts contain a combination of CRISPR-associated (Cas)genes as well as non-coding RNA elements capable of programming thespecificity of the CRISPR-mediated nucleic acid cleavage.

The Type II CRISPR is one of the most well characterized systems andcarries out targeted DNA double-strand break in four sequential steps.First, two non-coding RNA, the pre-crRNA array and tracrRNA, aretranscribed from the CRISPR locus. Second, tracrRNA hybridizes to therepeat regions of the pre-crRNA and mediates the processing of pre-crRNAinto mature crRNAs containing individual spacer sequences. Third, themature crRNA:tracrRNA complex directs functional domain (e.g., nucleasesuch as Cas) to the target DNA via Watson-Crick base-pairing between thespacer on the crRNA and the protospacer on the target DNA next to theprotospacer adjacent motif (PAM), an additional requirement for targetrecognition. Finally, Cas9 mediates cleavage of target DNA to create adouble-stranded break within the protospacer. Activity of the CRISPR/Cassystem comprises of three steps: (i) insertion of alien DNA sequencesinto the CRISPR array to prevent future attacks, in a process called‘adaptation’, (ii) expression of the relevant proteins, as well asexpression and processing of the array, followed by (iii) RNA-mediatedinterference with the alien nucleic acid. Thus, in the bacterial cell,several of the so-called ‘Cas’ proteins are involved with the naturalfunction of the CRISPR/Cas system and serve roles in functions such asinsertion of the alien DNA etc.

In certain embodiments, Cas protein may be a “functional derivative” ofa naturally occurring Cas protein. A “functional derivative” of a nativesequence polypeptide is a compound having a qualitative biologicalproperty in common with a native sequence polypeptide. “Functionalderivatives” include, but are not limited to, fragments of a nativesequence and derivatives of a native sequence polypeptide and itsfragments, provided that they have a biological activity in common witha corresponding native sequence polypeptide. A biological activitycontemplated herein is the ability of the functional derivative tohydrolyze a DNA substrate into fragments. The term “derivative”encompasses both amino acid sequence variants of polypeptide, covalentmodifications, and fusions thereof such as derivative Cas proteins.Suitable derivatives of a Cas polypeptide or a fragment thereof includebut are not limited to mutants, fusions, covalent modifications of Casprotein or a fragment thereof. Cas protein, which includes Cas proteinor a fragment thereof, as well as derivatives of Cas protein or afragment thereof, may be obtainable from a cell or synthesizedchemically or by a combination of these two procedures. The cell may bea cell that naturally produces Cas protein, or a cell that naturallyproduces Cas protein and is genetically engineered to produce theendogenous Cas protein at a higher expression level or to produce a Casprotein from an exogenously introduced nucleic acid, which nucleic acidencodes a Cas that is same or different from the endogenous Cas. In somecase, the cell does not naturally produce Cas protein and is geneticallyengineered to produce a Cas protein. In some embodiments, the Casprotein is a small Cas9 ortholog for delivery via an AAV vector (Ran etal. (2015) Nature 520:186).

In some embodiments, the DNA binding domain is part of a TtAgo system(see Swarts et al., ibid; Sheng et al., ibid). In eukaryotes, genesilencing is mediated by the Argonaute (Ago) family of proteins. In thisparadigm, Ago is bound to small (19-31 nt) RNAs. This protein-RNAsilencing complex recognizes target RNAs via Watson-Crick base pairingbetween the small RNA and the target and endonucleolytically cleaves thetarget RNA (Vogel (2014) Science 344:972-973). In contrast, prokaryoticAgo proteins bind to small single-stranded DNA fragments and likelyfunction to detect and remove foreign (often viral) DNA (Yuan et al.(2005) Mol. Cell 19:405; Olovnikov et al. (2013) Mol. Cell 51:594;Swarts et al., ibid). Exemplary prokaryotic Ago proteins include thosefrom Aquifex aeolicus, Rhodobacter sphaeroides, and Thermusthermophilus.

One of the most well-characterized prokaryotic Ago protein is the onefrom T. thermophilus (TtAgo; Swarts et al., ibid). TtAgo associates witheither 15 nt or 13-25 nt single-stranded DNA fragments with 5′ phosphategroups. This “guide DNA” bound by TtAgo serves to direct the protein-DNAcomplex to bind a Watson-Crick complementary DNA sequence in athird-party molecule of DNA. Once the sequence information in theseguide DNAs has allowed identification of the target DNA, the TtAgo-guideDNA complex cleaves the target DNA. Such a mechanism is also supportedby the structure of the TtAgo-guide DNA complex while bound to itstarget DNA (G. Sheng et al., ibid). Ago from Rhodobacter sphaeroides(RsAgo) has similar properties (Olovnikov et al., ibid).

Exogenous guide DNAs of arbitrary DNA sequence can be loaded onto theTtAgo protein (Swarts et al., ibid.). Since the specificity of TtAgocleavage is directed by the guide DNA, a TtAgo-DNA complex formed withan exogenous, investigator-specified guide DNA will therefore directTtAgo target DNA cleavage to a complementary investigator-specifiedtarget DNA. In this way, one may create a targeted double-strand breakin DNA. Use of the TtAgo-guide DNA system (or orthologous Ago-guide DNAsystems from other organisms) allows for targeted cleavage of genomicDNA within cells. Such cleavage can be either single- ordouble-stranded. For cleavage of mammalian genomic DNA, it would bepreferable to use of a version of TtAgo codon optimized for expressionin mammalian cells. Further, it might be preferable to treat cells witha TtAgo-DNA complex formed in vitro where the TtAgo protein is fused toa cell-penetrating peptide. Further, it might be preferable to use aversion of the TtAgo protein that has been altered via mutagenesis tohave improved activity at 37° C. Ago-RNA-mediated DNA cleavage could beused to affect a panopoly of outcomes including gene knock-out, targetedgene addition, gene correction, targeted gene deletion using techniquesstandard in the art for exploitation of DNA breaks.

Thus, any DNA-binding domain can be used.

Fusion Molecules

Fusion molecules comprising DNA-binding domains (e.g., ZFPs or TALEs,CRISPR/Cas components such as single guide RNAs) as described hereinassociated with a heterologous regulatory (functional) domain (orfunctional fragment thereof) are also provided. Common domains include,e.g., transcription factor domains (activators, repressors,co-activators, co-repressors), silencers, oncogenes (e.g., myc, jun,fos, myb, max, mad, rel, ets, bcl, myb, mos family members etc.); DNArepair enzymes and their associated factors and modifiers; DNArearrangement enzymes and their associated factors and modifiers;chromatin associated proteins and their modifiers (e.g. kinases,acetylases and deacetylases); and DNA modifying enzymes (e.g.,methyltransferases, topoisomerases, helicases, ligases, kinases,phosphatases, polymerases, endonucleases) and their associated factorsand modifiers. Such fusion molecules include transcription factorscomprising the DNA-binding domains described herein and atranscriptional regulatory domain as well as nucleases comprising theDNA-binding domains and one or more nuclease domains.

Suitable domains for achieving activation (transcriptional activationdomains) include the HSV VP16 activation domain (see, e.g., Hagmann etal. (1997) J. Virol. 71:5952-5962) nuclear hormone receptors (see, e.g.,Torchia et al. (1998) Curr. Opin. Cell. Biol. 10:373-383); the p65subunit of nuclear factor kappa B (Bitko & Barik (1998) J. Virol.72:5610-5618 and Doyle & Hunt (1997) Neuroreport 8:2937-2942); Liu etal. (1998) Cancer Gene Ther. 5:3-28), or artificial chimeric functionaldomains such as VP64 (Beerli et al. (1998) Proc. Natl. Acad. Sci. USA95:14623-33), and degron (Molinari et al. (1999) EMBO J. 18:6439-6447).Additional exemplary activation domains include, Oct 1, Oct-2A, Sp1,AP-2, and CTF1 (Seipel et al. (1992) EMBO J. 11:4961-4968) as well asp300, CBP, PCAF, SRC1 PvALF, AtHD2A and ERF-2. See, for example, Robyret al. (2000) Mol. Endocrinol. 14:329-347; Collingwood et al. (1999) J.Mol. Endocrinol. 23:255-275; Leo et al. (2000) Gene 245:1-11;Manteuffel-Cymborowska (1999) Acta Biochim. Pol. 46:77-89; McKenna etal. (1999) J. Steroid Biochem. Mol. Biol. 69:3-12; Malik et al. (2000)Trends Biochem. Sci. 25:277-283; and Lemon et al. (1999) Curr. Opin.Genet. Dev. 9:499-504. Additional exemplary activation domains include,but are not limited to, OsGAI, HALF-1, C1, AP1, ARF-5, -6, -7, and -8,CPRF1, CPRF4, MYC-RP/GP, and TRAB1. See, for example, Ogawa et al.(2000) Gene 245:21-29; Okanami et al. (1996) Genes Cells 1:87-99; Goffet al. (1991) Genes Dev. 5:298-309; Cho et al. (1999) Plant Mol. Biol.40:419-429; Ulmason et al. (1999) Proc. Natl. Acad. Sci. USA96:5844-5849; Sprenger-Haussels et al. (2000) Plant J. 22:1-8; Gong etal. (1999) Plant Mol. Biol. 41:33-44; and Hobo et al. (1999) Proc. Natl.Acad. Sci. USA 96:15,348-15,353.

It will be clear to those of skill in the art that, in the formation ofa fusion protein (or a nucleic acid encoding same) between a DNA-bindingdomain and a functional domain, either an activation domain or amolecule that interacts with an activation domain is suitable as afunctional domain. Essentially any molecule capable of recruiting anactivating complex and/or activating activity (such as, for example,histone acetylation) to the target gene is useful as an activatingdomain of a fusion protein. Insulator domains, localization domains, andchromatin remodeling proteins such as ISWI-containing domains and/ormethyl binding domain proteins suitable for use as functional domains infusion molecules are described, for example, in U.S. Pat. No. 7,053,264.

Exemplary repression domains include, but are not limited to, KRAB A/B,KOX, TGF-beta-inducible early gene (TIEG), v-erbA, SID, MBD2, MBD3,members of the DNMT family (e.g., DNMT1, DNMT3A, DNMT3B), Rb, and MeCP2.See, for example, Bird et al. (1999) Cell 99:451-454; Tyler et al.(1999) Cell 99:443-446; Knoepfler et al. (1999) Cell 99:447-450; andRobertson et al. (2000) Nature Genet. 25:338-342. Additional exemplaryrepression domains include, but are not limited to, ROM2 and AtHD2A.See, for example, Chem et al. (1996) Plant Cell 8:305-321; and Wu et al.(2000) Plant J. 22:19-27.

Fusion molecules are constructed by methods of cloning and biochemicalconjugation that are well known to those of skill in the art. Fusionmolecules comprise a DNA-binding domain (e.g., ZFP, TALE, sgRNA) and afunctional domain (e.g., a transcriptional activation or repressiondomain). Fusion molecules also optionally comprise nuclear localizationsignals (such as, for example, that from the SV40 medium T-antigen) andepitope tags (such as, for example, FLAG and hemagglutinin). Fusionproteins (and nucleic acids encoding them) are designed such that thetranslational reading frame is preserved among the components of thefusion.

Fusions between a polypeptide component of a functional domain (or afunctional fragment thereof) on the one hand, and a non-proteinDNA-binding domain (e.g., antibiotic, intercalator, minor groove binder,nucleic acid) on the other, are constructed by methods of biochemicalconjugation known to those of skill in the art. See, for example, thePierce Chemical Company (Rockford, Ill.) Catalogue. Methods andcompositions for making fusions between a minor groove binder and apolypeptide have been described. Mapp et al. (2000) Proc. Natl. Acad.Sci. USA 97:3930-3935. Furthermore, single guide RNAs of the CRISPR/Cassystem associate with functional domains to form active transcriptionalregulators and nucleases.

In certain embodiments, the target site is present in an accessibleregion of cellular chromatin. Accessible regions can be determined asdescribed, for example, in U.S. Pat. Nos. 7,217,509 and 7,923,542. Ifthe target site is not present in an accessible region of cellularchromatin, one or more accessible regions can be generated as describedin U.S. Pat. Nos. 7,785,792 and 8,071,370. In additional embodiments,the DNA-binding domain of a fusion molecule is capable of binding tocellular chromatin regardless of whether its target site is in anaccessible region or not. For example, such DNA-binding domains arecapable of binding to linker DNA and/or nucleosomal DNA. Examples ofthis type of “pioneer” DNA binding domain are found in certain steroidreceptor and in hepatocyte nuclear factor 3 (HNF3) (Cordingley et al.(1987) Cell 48:261-270; Pina et al. (1990) Cell 60:719-731; and Cirilloet al. (1998) EMBO J. 17:244-254).

The fusion molecule may be formulated with a pharmaceutically acceptablecarrier, as is known to those of skill in the art. See, for example,Remington's Pharmaceutical Sciences, 17th ed., 1985; and U.S. Pat. Nos.6,453,242 and 6,534,261.

The functional component/domain of a fusion molecule can be selectedfrom any of a variety of different components capable of influencingtranscription of a gene once the fusion molecule binds to a targetsequence via its DNA binding domain. Hence, the functional component caninclude, but is not limited to, various transcription factor domains,such as activators, repressors, co-activators, co-repressors, andsilencers.

Additional exemplary functional domains are disclosed, for example, inU.S. Pat. Nos. 6,534,261 and 6,933,113.

Functional domains that are regulated by exogenous small molecules orligands may also be selected. For example, RheoSwitch® technology may beemployed wherein a functional domain only assumes its activeconformation in the presence of the external RheoChem™ ligand (see forexample U.S. Patent Publication No. 2009/0136465). Thus, the ZFP may beoperably linked to the regulatable functional domain wherein theresultant activity of the ZFP-TF is controlled by the external ligand.

Nucleases

In certain embodiments, the fusion molecule comprises a DNA-bindingbinding domain associated with a cleavage (nuclease) domain. As such,gene modification can be achieved using a nuclease, for example anengineered nuclease. Engineered nuclease technology is based on theengineering of naturally occurring DNA-binding proteins. For example,engineering of homing endonucleases with tailored DNA-bindingspecificities has been described. Chames et al. (2005) Nucleic Acids Res33(20):e178; Arnould et al. (2006) J. Mol. Biol. 355:443-458. Inaddition, engineering of ZFPs has also been described. See, e.g., U.S.Pat. Nos. 6,534,261; 6,607,882; 6,824,978; 6,979,539; 6,933,113;7,163,824; and 7,013,219.

In addition, ZFPs and/or TALEs can be fused to nuclease domains tocreate ZFNs and TALENs—a functional entity that is able to recognize itsintended nucleic acid target through its engineered (ZFP or TALE) DNAbinding domain and cause the DNA to be cut near the DNA binding site viathe nuclease activity.

Thus, the methods and compositions described herein are broadlyapplicable and may involve any nuclease of interest. Non-limitingexamples of nucleases include meganucleases, TALENs and zinc fingernucleases. The nuclease may comprise heterologous DNA-binding andcleavage domains (e.g., zinc finger nucleases; meganuclease DNA-bindingdomains with heterologous cleavage domains) or, alternatively, theDNA-binding domain of a naturally-occurring nuclease may be altered tobind to a selected target site (e.g., a meganuclease that has beenengineered to bind to site different than the cognate binding site).

In any of the nucleases described herein, the nuclease can comprise anengineered TALE DNA-binding domain and a nuclease domain (e.g.,endonuclease and/or meganuclease domain), also referred to as TALENs.Methods and compositions for engineering these TALEN proteins forrobust, site specific interaction with the target sequence of the user'schoosing have been published (see U.S. Pat. No. 8,586,526). In someembodiments, the TALEN comprises an endonuclease (e.g., FokI) cleavagedomain or cleavage half-domain. In other embodiments, the TALE-nucleaseis a mega TAL. These mega TAL nucleases are fusion proteins comprising aTALE DNA binding domain and a meganuclease cleavage domain. Themeganuclease cleavage domain is active as a monomer and does not requiredimerization for activity. (See Boissel et al. (2013) Nucl Acid Res:1-13, doi: 10.1093/nar/gkt1224). In addition, the nuclease domain mayalso exhibit DNA-binding functionality.

In still further embodiments, the nuclease comprises a compact TALEN(cTALEN). These are single chain fusion proteins linking a TALE DNAbinding domain to a TevI nuclease domain. The fusion protein can act aseither a nickase localized by the TALE region, or can create a doublestrand break, depending upon where the TALE DNA binding domain islocated with respect to the TevI nuclease domain (see Beurdeley et al.(2013) Nat Comm 1:8 DOI: 10.1038/ncomms2782). Any TALENs may be used incombination with additional TALENs (e.g., one or more TALENs (cTALENs orFokI-TALENs) with one or more mega-TALs) or other DNA cleavage enzymes.

In certain embodiments, the nuclease comprises a meganuclease (homingendonuclease) or a portion thereof that exhibits cleavage activity.Naturally-occurring meganucleases recognize 15-40 base-pair cleavagesites and are commonly grouped into four families: the LAGLIDADG family(“LAGLIDADG” disclosed as SEQ ID NO: 227), the GIY-YIG family, theHis-Cyst box family and the HNH family. Exemplary homing endonucleasesinclude I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI,I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII. Theirrecognition sequences are known. See also U.S. Pat. Nos. 5,420,032;6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujonet al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res.22:1125-1127; Jasin (1996) Trends Genet. 12:224-28; Gimble et al. (1996)J. Mol. Biol. 263:163-80; Argast et al. (1998) J. Mol. Biol. 280:345-353and the New England Biolabs catalogue.

DNA-binding domains from naturally-occurring meganucleases, primarilyfrom the LAGLIDADG family (“LAGLIDADG” disclosed as SEQ ID NO: 227),have been used to promote site-specific genome modification in plants,yeast, Drosophila, mammalian cells and mice, but this approach has beenlimited to the modification of either homologous genes that conserve themeganuclease recognition sequence (Monet et al. (1999) Biochem.Biophysics. Res. Common. 255:88-93) or to pre-engineered genomes intowhich a recognition sequence has been introduced (Route et al. (1994),Mol. Cell. Biol. 14:8096-106; Chilton et al. (2003) Plant Physiology.133:956-65; Puchta et al. (1996) Proc. Natl. Acad. Sci. USA 93:5055-60;Rong et al. (2002) Genes Dev. 16:1568-81; Gouble et al. (2006) J. GeneMed. 8(5):616-622). Accordingly, attempts have been made to engineermeganucleases to exhibit novel binding specificity at medically orbiotechnologically relevant sites (Porteus et al. (2005) Nat.Biotechnol. 23:967-73; Sussman et al. (2004) J. Mol. Biol. 342:31-41;Epinat et al. (2003) Nucleic Acids Res. 31:2952-62; Chevalier et al.(2002) Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic Acids Res.31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques et al.(2007) Current Gene Therapy 7:49-66; U.S. Patent Publication Nos.2007/0117128; 2006/0206949; 2006/0153826; 2006/0078552; and2004/0002092). In addition, naturally-occurring or engineeredDNA-binding domains from meganucleases can be operably linked with acleavage domain from a heterologous nuclease (e.g., FokI) and/orcleavage domains from meganucleases can be operably linked with aheterologous DNA-binding domain (e.g., ZFP or TALE).

In other embodiments, the nuclease is a zinc finger nuclease (ZFN) orTALE DNA binding domain-nuclease fusion (TALEN). ZFNs and TALENscomprise a DNA binding domain (zinc finger protein or TALE DNA bindingdomain) that has been engineered to bind to a target site in a gene ofchoice and cleavage domain or a cleavage half-domain (e.g., from arestriction and/or meganuclease as described herein).

As described in detail above, zinc finger binding domains and TALE DNAbinding domains can be engineered to bind to a sequence of choice. See,for example, Beerli et al. (2002) Nature Biotechnol. 20:135-141; Pabo etal. (2001) Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001) NatureBiotechnol. 19:656-660; Segal et al. (2001) Curr. Opin. Biotechnol.12:632-637; Choo et al. (2000) Curr. Opin. Struct. Biol. 10:411-416. Anengineered zinc finger binding domain or TALE protein can have a novelbinding specificity, compared to a naturally-occurring protein.Engineering methods include, but are not limited to, rational design andvarious types of selection. Rational design includes, for example, usingdatabases comprising triplet (or quadruplet) nucleotide sequences andindividual zinc finger or TALE amino acid sequences, in which eachtriplet or quadruplet nucleotide sequence is associated with one or moreamino acid sequences of zinc fingers or TALE repeat units which bind theparticular triplet or quadruplet sequence. See, for example, U.S. Pat.Nos. 6,453,242 and 6,534,261, incorporated by reference herein in theirentireties.

Selection of target sites; and methods for design and construction offusion proteins (and polynucleotides encoding same) are known to thoseof skill in the art and described in detail in U.S. Pat. Nos. 7,888,121and 8,409,861, incorporated by reference in their entireties herein.

In addition, as disclosed in these and other references, zinc fingerdomains, TALEs and/or multi-fingered zinc finger proteins may be linkedtogether using any suitable linker sequences, including for example,linkers of 5 or more amino acids in length. See, e.g., U.S. Pat. Nos.6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 ormore amino acids in length. The proteins described herein may includeany combination of suitable linkers between the individual zinc fingersof the protein. See, also, U.S. Pat. No. 8,772,453.

Thus, nucleases such as ZFNs, TALENs and/or meganucleases can compriseany DNA-binding domain and any nuclease (cleavage) domain (cleavagedomain, cleavage half-domain). As noted above, the cleavage domain maybe heterologous to the DNA-binding domain, for example a zinc finger orTAL-effector DNA-binding domain and a cleavage domain from a nuclease ora meganuclease DNA-binding domain and cleavage domain from a differentnuclease. Heterologous cleavage domains can be obtained from anyendonuclease or exonuclease. Exemplary endonucleases from which acleavage domain can be derived include, but are not limited to,restriction endonucleases and homing endonucleases. See, for example,2002-2003 Catalogue, New England Biolabs, Beverly, Mass.; and Belfort etal. (1997) Nucleic Acids Res. 25:3379-3388. Additional enzymes whichcleave DNA are known (e.g., S1 Nuclease; mung bean nuclease; pancreaticDNase I; micrococcal nuclease; yeast HO endonuclease; see also Linn etal. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). One ormore of these enzymes (or functional fragments thereof) can be used as asource of cleavage domains and cleavage half-domains.

Similarly, a cleavage half-domain can be derived from any nuclease orportion thereof, as set forth above, that requires dimerization forcleavage activity. In general, two fusion proteins are required forcleavage if the fusion proteins comprise cleavage half-domains.Alternatively, a single protein comprising two cleavage half-domains canbe used. The two cleavage half-domains can be derived from the sameendonuclease (or functional fragments thereof), or each cleavagehalf-domain can be derived from a different endonuclease (or functionalfragments thereof). In addition, the target sites for the two fusionproteins are preferably disposed, with respect to each other, such thatbinding of the two fusion proteins to their respective target sitesplaces the cleavage half-domains in a spatial orientation to each otherthat allows the cleavage half-domains to form a functional cleavagedomain, e.g., by dimerizing. Thus, in certain embodiments, the nearedges of the target sites are separated by 5-8 nucleotides or by 15-18nucleotides. However, any integral number of nucleotides or nucleotidepairs can intervene between two target sites (e.g., from 2 to 50nucleotide pairs or more). In general, the site of cleavage lies betweenthe target sites, but may lie 1 or more kilobases away from the cleavagesite, including between 1-50 base pairs (or any value therebetweenincluding 1-5, 1-10, and 1-20 base pairs), 1-100 base pairs (or anyvalue therebetween), 100-500 base pairs (or any value therebetween), 500to 1000 base pairs (or any value therebetween) or even more than 1 kbfrom the cleavage site.

Restriction endonucleases (restriction enzymes) are present in manyspecies and are capable of sequence-specific binding to DNA (at arecognition site), and cleaving DNA at or near the site of binding.Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removedfrom the recognition site and have separable binding and cleavagedomains. For example, the Type IIS enzyme FokI catalyzes double-strandedcleavage of DNA, at 9 nucleotides from its recognition site on onestrand and 13 nucleotides from its recognition site on the other. See,for example, U.S. Pat. Nos. 5,356,802; 5,436,150; and 5,487,994; as wellas Li et al. (1992) Proc. Natl. Acad Sci. USA 89:4275-4279; Li et al.(1993) Proc. Natl. Acad Sci. USA 90:2764-2768; Kim et al. (1994a) Proc.Natl. Acad Sci. USA 91:883-887; Kim et al. (1994b) J. Biol. Chem.269:31,978-31,982. Thus, in one embodiment, fusion proteins comprise thecleavage domain (or cleavage half-domain) from at least one Type IISrestriction enzyme and one or more zinc finger binding domains, whichmay or may not be engineered.

An exemplary Type IIS restriction enzyme, whose cleavage domain isseparable from the binding domain, is FokI. This particular enzyme isactive as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad Sci. USA 95:10,570-10,575. Accordingly, for the purposes of the present disclosure,the portion of the FokI enzyme used in the disclosed fusion proteins isconsidered a cleavage half-domain. Thus, for targeted double-strandedcleavage and/or targeted replacement of cellular sequences using zincfinger-FokI fusions, two fusion proteins, each comprising a FokIcleavage half-domain, can be used to reconstitute a catalytically activecleavage domain. Alternatively, a single polypeptide molecule containinga zinc finger binding domain and two FokI cleavage half-domains can alsobe used. Parameters for targeted cleavage and targeted sequencealteration using zinc finger-FokI fusions are provided elsewhere in thisdisclosure.

A cleavage domain or cleavage half-domain can be any portion of aprotein that retains cleavage activity, or that retains the ability tomultimerize (e.g., dimerize) to form a functional cleavage domain.

Exemplary Type IIS restriction enzymes are described in InternationalPatent Publication No. WO 07/014275, incorporated herein in itsentirety. Additional restriction enzymes also contain separable bindingand cleavage domains, and these are contemplated by the presentdisclosure. See, for example, Roberts et al. (2003) Nucleic Acids Res.31:418-420.

In certain embodiments, the cleavage domain comprises one or moreengineered cleavage half-domain (also referred to as dimerization domainmutants) that minimize or prevent homodimerization, as described, forexample, in U.S. Pat. Nos. 7,914,796; 8,034,598 and 8,623,618; and U.S.Patent Publication No. 2011/0201055, the disclosures of all of which areincorporated by reference in their entireties herein. Amino acidresidues at positions 446, 447, 479, 483, 484, 486, 487, 490, 491, 496,498, 499, 500, 531, 534, 537, and 538 of FokI are all targets forinfluencing dimerization of the FokI cleavage half-domains.

Exemplary engineered cleavage half-domains of FokI that form obligateheterodimers include a pair in which a first cleavage half-domainincludes mutations at amino acid residues at positions 490 and 538 ofFokI and a second cleavage half-domain includes mutations at amino acidresidues 486 and 499.

Thus, in one embodiment, a mutation at 490 replaces Glu (E) with Lys(K); the mutation at 538 replaces Iso (I) with Lys (K); the mutation at486 replaced Gln (Q) with Glu (E); and the mutation at position 499replaces Iso (I) with Lys (K). Specifically, the engineered cleavagehalf-domains described herein were prepared by mutating positions 490(E→K) and 538 (I→K) in one cleavage half-domain to produce an engineeredcleavage half-domain designated “E490K:I538K” and by mutating positions486 (Q→E) and 499 (I→L) in another cleavage half-domain to produce anengineered cleavage half-domain designated “Q486E:I499L”. The engineeredcleavage half-domains described herein are obligate heterodimer mutantsin which aberrant cleavage is minimized or abolished. See, e.g., U.S.Pat. Nos. 7,914,796 and 8,034,598, the disclosures of which areincorporated by reference in its entirety for all purposes. In certainembodiments, the engineered cleavage half-domain comprises mutations atpositions 486, 499 and 496 (numbered relative to wild-type FokI), forinstance mutations that replace the wild type Gln (Q) residue atposition 486 with a Glu (E) residue, the wild type Iso (I) residue atposition 499 with a Leu (L) residue and the wild-type Asn (N) residue atposition 496 with an Asp (D) or Glu (E) residue (also referred to as a“ELD” and “ELE” domains, respectively). In other embodiments, theengineered cleavage half-domain comprises mutations at positions 490,538 and 537 (numbered relative to wild-type FokI), for instancemutations that replace the wild type Glu (E) residue at position 490with a Lys (K) residue, the wild type Iso (I) residue at position 538with a Lys (K) residue, and the wild-type His (H) residue at position537 with a Lys (K) residue or a Arg (R) residue (also referred to as“KKK” and “KKR” domains, respectively). In other embodiments, theengineered cleavage half-domain comprises mutations at positions 490 and537 (numbered relative to wild-type FokI), for instance mutations thatreplace the wild type Glu (E) residue at position 490 with a Lys (K)residue and the wild-type His (H) residue at position 537 with a Lys (K)residue or a Arg (R) residue (also referred to as “KIK” and “KIR”domains, respectively). See, e.g., U.S. Pat. Nos. 7,914,796; 8,034,598;and 8,623,618, the disclosures of which are incorporated by reference inits entirety for all purposes. In other embodiments, the engineeredcleavage half domain comprises the “Sharkey” and/or “Sharkey mutations”(see Guo et al. (2010) J. Mol. Biol. 400(1):96-107).

Alternatively, nucleases may be assembled in vivo at the nucleic acidtarget site using so-called “split-enzyme” technology (see e.g. U.S.Patent Publication No. 2009/0068164). Components of such split enzymesmay be expressed either on separate expression constructs, or can belinked in one open reading frame where the individual components areseparated, for example, by a self-cleaving 2A peptide or IRES sequence.Components may be individual zinc finger binding domains or domains of ameganuclease nucleic acid binding domain.

Nucleases (e.g., ZFNs and/or TALENs) can be screened for activity priorto use, for example in a yeast-based chromosomal system as described inas described in U.S. Pat. No. 8,563,314.

In certain embodiments, the nuclease comprises a CRISPR/Cas system. TheCRISPR (clustered regularly interspaced short palindromic repeats)locus, which encodes RNA components of the system, and the Cas(CRISPR-associated) locus, which encodes proteins (Jansen et al. (2002)Mol. Microbiol. 43:1565-1575; Makarova et al. (2002) Nucleic Acids Res.30:482-496; Makarova et al. (2006) Biol. Direct 1:7; Haft et al. (2005)PLoS Comput. Biol. 1:e60) make up the gene sequences of the CRISPR/Casnuclease system. CRISPR loci in microbial hosts contain a combination ofCRISPR-associated (Cas) genes as well as non-coding RNA elements capableof programming the specificity of the CRISPR-mediated nucleic acidcleavage.

The Type II CRISPR is one of the most well characterized systems andcarries out targeted DNA double-strand break in four sequential steps.First, two non-coding RNA, the pre-crRNA array and tracrRNA, aretranscribed from the CRISPR locus. Second, tracrRNA hybridizes to therepeat regions of the pre-crRNA and mediates the processing of pre-crRNAinto mature crRNAs containing individual spacer sequences. Third, themature crRNA:tracrRNA complex directs Cas9 to the target DNA viaWatson-Crick base-pairing between the spacer on the crRNA and theprotospacer on the target DNA next to the protospacer adjacent motif(PAM), an additional requirement for target recognition. Finally, Cas9mediates cleavage of target DNA to create a double-stranded break withinthe protospacer. Activity of the CRISPR/Cas system comprises of threesteps: (i) insertion of alien DNA sequences into the CRISPR array toprevent future attacks, in a process called ‘adaptation’, (ii)expression of the relevant proteins, as well as expression andprocessing of the array, followed by (iii) RNA-mediated interferencewith the alien nucleic acid. Thus, in the bacterial cell, several of theso-called ‘Cas’ proteins are involved with the natural function of theCRISPR/Cas system and serve roles in functions such as insertion of thealien DNA etc.

In some embodiments, the CRISPR-Cpf1 system is used. The CRISPR-Cpf1system, identified in Francisella spp, is a class 2 CRISPR-Cas systemthat mediates robust DNA interference in human cells. Althoughfunctionally conserved, Cpf1 and Cas9 differ in many aspects includingin their guide RNAs and substrate specificity (see Fagerlund et al.(2015) Genom Bio 16:251). A major difference between Cas9 and Cpf1proteins is that Cpf1 does not utilize tracrRNA, and thus requires onlya crRNA. The FnCpf1 crRNAs are 42-44 nucleotides long (19-nucleotiderepeat and 23-25-nucleotide spacer) and contain a single stem-loop,which tolerates sequence changes that retain secondary structure. Inaddition, the Cpf1 crRNAs are significantly shorter than the˜100-nucleotide engineered sgRNAs required by Cas9, and the PAMrequirements for FnCpf1 are 5′-TTN-3′ and 5′-CTA-3′ on the displacedstrand. Although both Cas9 and Cpf1 make double strand breaks in thetarget DNA, Cas9 uses its RuvC- and HNH-like domains to make blunt-endedcuts within the seed sequence of the guide RNA, whereas Cpf1 uses aRuvC-like domain to produce staggered cuts outside of the seed. BecauseCpf1 makes staggered cuts away from the critical seed region, NHEJ willnot disrupt the target site, therefore ensuring that Cpf1 can continueto cut the same site until the desired HDR recombination event has takenplace. Thus, in the methods and compositions described herein, it isunderstood that the term “‘Cas” includes both Cas9 and Cpf1 proteins.Thus, as used herein, a “CRISPR/Cas system” refers both CRISPR/Casand/or CRISPR/Cpf1 systems, including both nuclease and/or transcriptionfactor systems.

In certain embodiments, Cas protein may be a “functional derivative” ofa naturally occurring Cas protein. A “functional derivative” of a nativesequence polypeptide is a compound having a qualitative biologicalproperty in common with a native sequence polypeptide. “Functionalderivatives” include, but are not limited to, fragments of a nativesequence and derivatives of a native sequence polypeptide and itsfragments, provided that they have a biological activity in common witha corresponding native sequence polypeptide. A biological activitycontemplated herein is the ability of the functional derivative tohydrolyze a DNA substrate into fragments. The term “derivative”encompasses both amino acid sequence variants of polypeptide, covalentmodifications, and fusions thereof. Suitable derivatives of a Caspolypeptide or a fragment thereof include but are not limited tomutants, fusions, covalent modifications of Cas protein or a fragmentthereof. Cas protein, which includes Cas protein or a fragment thereof,as well as derivatives of Cas protein or a fragment thereof, may beobtainable from a cell or synthesized chemically or by a combination ofthese two procedures. The cell may be a cell that naturally produces Casprotein, or a cell that naturally produces Cas protein and isgenetically engineered to produce the endogenous Cas protein at a higherexpression level or to produce a Cas protein from an exogenouslyintroduced nucleic acid, which nucleic acid encodes a Cas that is sameor different from the endogenous Cas. In some case, the cell does notnaturally produce Cas protein and is genetically engineered to produce aCas protein.

Exemplary CRISPR/Cas nuclease systems targeted to TCR genes and othergenes are disclosed for example, in U.S. Patent Publication No.2015/0056705.

The nuclease(s) may make one or more double-stranded and/orsingle-stranded cuts in the target site. In certain embodiments, thenuclease comprises a catalytically inactive cleavage domain (e.g., FokIand/or Cas protein). See, e.g., U.S. Pat. Nos. 9,200,266 and 8,703,489and Guillinger et al. (2014) Nature Biotech. 32(6):577-582. Thecatalytically inactive cleavage domain may, in combination with acatalytically active domain act as a nickase to make a single-strandedcut. Therefore, two nickases can be used in combination to make adouble-stranded cut in a specific region. Additional nickases are alsoknown in the art, for example, McCaffrey et al. (2016) Nucleic AcidsRes. 44(2):e11. doi: 10.1093/nar/gkv878. Epub 2015 Oct. 19.

Delivery

The proteins (e.g., transcription factors, nucleases, TCR and CARmolecules), polynucleotides and/or compositions comprising the proteinsand/or polynucleotides described herein may be delivered to a targetcell by any suitable means, including, for example, by injection of theprotein and/or mRNA components.

Suitable cells include but not limited to eukaryotic and prokaryoticcells and/or cell lines. Non-limiting examples of such cells or celllines generated from such cells include T-cells, COS, CHO (e.g., CHO-S,CHO-K1, CHO-DG44, CHO-DUXB11, CHO-DUKX, CHOK1SV), VERO, MDCK, WI38, V79,B14AF28-G3, BHK, HaK, NS0, SP2/0-Ag14, HeLa, HEK293 (e.g., HEK293-F,HEK293-H, HEK293-T), and perC6 cells as well as insect cells such asSpodoptera frugiperda (Sf), or fungal cells such as Saccharomyces,Pichia and Schizosaccharomyces. In certain embodiments, the cell line isa CHO-K1, MDCK or HEK293 cell line. Suitable cells also include stemcells such as, by way of example, embryonic stem cells, inducedpluripotent stem cells (iPS cells), hematopoietic stem cells, neuronalstem cells and mesenchymal stem cells.

Methods of delivering proteins comprising DNA-binding domains asdescribed herein are described, for example, in U.S. Pat. Nos.6,453,242; 6,503,717; 6,534,261; 6,599,692; 6,607,882; 6,689,558;6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824, thedisclosures of all of which are incorporated by reference herein intheir entireties.

DNA binding domains and fusion proteins comprising these DNA bindingdomains as described herein may also be delivered using vectorscontaining sequences encoding one or more of the DNA-binding protein(s).Additionally, additional nucleic acids (e.g., donors) also may bedelivered via these vectors. Any vector systems may be used including,but not limited to, plasmid vectors, retroviral vectors, lentiviralvectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors andadeno-associated virus vectors, etc. See, also, U.S. Pat. Nos.6,534,261; 6,607,882; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and7,163,824, incorporated by reference herein in their entireties.Furthermore, it will be apparent that any of these vectors may compriseone or more DNA-binding protein-encoding sequences and/or additionalnucleic acids as appropriate. Thus, when one or more DNA-bindingproteins as described herein are introduced into the cell, andadditional DNAs as appropriate, they may be carried on the same vectoror on different vectors. When multiple vectors are used, each vector maycomprise a sequence encoding one or multiple DNA-binding proteins andadditional nucleic acids as desired.

Conventional viral and non-viral based gene transfer methods can be usedto introduce nucleic acids encoding engineered DNA-binding proteins incells (e.g., mammalian cells) and target tissues and to co-introduceadditional nucleotide sequences as desired. Such methods can also beused to administer nucleic acids (e.g., encoding DNA-binding proteinsand/or donors) to cells in vitro. In certain embodiments, nucleic acidsare administered for in vivo or ex vivo gene therapy uses. Non-viralvector delivery systems include DNA plasmids, naked nucleic acid, andnucleic acid complexed with a delivery vehicle such as a liposome, lipidnanoparticle or poloxamer. Viral vector delivery systems include DNA andRNA viruses, which have either episomal or integrated genomes afterdelivery to the cell. For a review of gene therapy procedures, seeAnderson (1992) Science 256:808-813; Nabel & Felgner (1993) TIBTECH11:211-217; Mitani & Caskey (1993) TIBTECH 11:162-166; Dillon (1993)TIBTECH 11:167-175; Miller (1992) Nature 357:455-460; Van Brunt (1988)Biotechnology 6(10):1149-1154; Vigne (1995) Restorative Neurology andNeuroscience 8:35-36; Kremer & Perricaudet (1995) British MedicalBulletin 51(1):31-44; Haddada et al., in Current Topics in Microbiologyand Immunology Doerfler and Böhm (eds.) (1995); and Yu et al. (1994)Gene Therapy 1:13-26.

Methods of non-viral delivery of nucleic acids include electroporation,lipofection, microinjection, biolistics, virosomes, liposomes, lipidnanoparticles, immunoliposomes, polycation or lipid:nucleic acidconjugates, naked DNA, mRNA, artificial virions, and agent-enhanceduptake of DNA. Sonoporation using, e.g., the Sonitron 2000 system(Rich-Mar) can also be used for delivery of nucleic acids. In apreferred embodiment, one or more nucleic acids are delivered as mRNA.Also preferred is the use of capped mRNAs to increase translationalefficiency and/or mRNA stability. Especially preferred are ARCA(anti-reverse cap analog) caps or variants thereof. See U.S. Pat. Nos.7,074,596 and 8,153,773, incorporated by reference herein.

Additional exemplary nucleic acid delivery systems include thoseprovided by Amaxa Biosystems (Cologne, Germany), Maxcyte, Inc.(Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) andCopernicus Therapeutics Inc, (see for example U.S. Pat. No. 6,008,336).Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386; 4,946,787;and 4,897,355) and lipofection reagents are sold commercially (e.g.,Transfectam™, Lipofectin™, and Lipofectamine™ RNAiMAX). Cationic andneutral lipids that are suitable for efficient receptor-recognitionlipofection of polynucleotides include those of Felgner, InternationalPatent Publication Nos. WO 91/17424 and WO 91/16024. Delivery can be tocells (ex vivo administration) or target tissues (in vivoadministration).

The preparation of lipid:nucleic acid complexes, including targetedliposomes such as immunolipid complexes, is well known to one of skillin the art (see, e.g., Crystal (1995) Science 270:404-410; Blaese et al.(1995) Cancer Gene Ther. 2:291-297; Behr et al. (1994) BioconjugateChem. 5:382-389; Remy et al. (1994) Bioconjugate Chem. 5:647-654; Gao etal. (1995) Gene Therapy 2:710-722; Ahmad et al. (1992) Cancer Res.52:4817-4820; U.S. Pat. Nos. 4,186,183; 4,217,344; 4,235,871; 4,261,975;4,485,054; 4,501,728; 4,774,085; 4,837,028; and 4,946,787).

Additional methods of delivery include the use of packaging the nucleicacids to be delivered into EnGeneIC delivery vehicles (EDVs). These EDVsare specifically delivered to target tissues using bispecific antibodieswhere one arm of the antibody has specificity for the target tissue andthe other has specificity for the EDV. The antibody brings the EDVs tothe target cell surface and then the EDV is brought into the cell byendocytosis. Once in the cell, the contents are released (see MacDiarmidet al. (2009) Nature Biotechnology 27(7):643).

The use of RNA or DNA viral based systems for the delivery of nucleicacids encoding engineered DNA-binding proteins, and/or donors (e.g. CARsor ACTRs) as desired takes advantage of highly evolved processes fortargeting a virus to specific cells in the body and trafficking theviral payload to the nucleus. Viral vectors can be administered directlyto patients (in vivo) or they can be used to treat cells in vitro andthe modified cells are administered to patients (ex vivo). Conventionalviral based systems for the delivery of nucleic acids include, but arenot limited to, retroviral, lentivirus, adenoviral, adeno-associated,vaccinia and herpes simplex virus vectors for gene transfer. Integrationin the host genome is possible with the retrovirus, lentivirus, andadeno-associated virus gene transfer methods, often resulting in longterm expression of the inserted transgene. Additionally, hightransduction efficiencies have been observed in many different celltypes and target tissues.

The tropism of a retrovirus can be altered by incorporating foreignenvelope proteins, expanding the potential target population of targetcells. Lentiviral vectors are retroviral vectors that are able totransduce or infect non-dividing cells and typically produce high viraltiters. Selection of a retroviral gene transfer system depends on thetarget tissue. Retroviral vectors are comprised of cis-acting longterminal repeats with packaging capacity for up to 6-10 kb of foreignsequence. The minimum cis-acting LTRs are sufficient for replication andpackaging of the vectors, which are then used to integrate thetherapeutic gene into the target cell to provide permanent transgeneexpression. Widely used retroviral vectors include those based uponmurine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), SimianImmunodeficiency virus (SIV), human immunodeficiency virus (HIV), andcombinations thereof (see, e.g., Buchscher et al. (1992) J. Virol.66:2731-2739; Johann et al. (1992) J. Virol. 66:1635-1640; Sommerfelt etal. (1990) Virol. 176:58-59; Wilson et al. (1989) J. Virol.63:2374-2378; Miller et al. (1991) J. Virol. 65:2220-2224; andInternational Patent Publication No. WO 94/26877).

In applications in which transient expression is preferred, adenoviralbased systems can be used. Adenoviral based vectors are capable of veryhigh transduction efficiency in many cell types and do not require celldivision. With such vectors, high titer and high levels of expressionhave been obtained. This vector can be produced in large quantities in arelatively simple system. Adeno-associated virus (“AAV”) vectors arealso used to transduce cells with target nucleic acids, e.g., in the invitro production of nucleic acids and peptides, and for in vivo and exvivo gene therapy procedures (see, e.g., West et al. (1987) Virology160:38-47; U.S. Pat. No. 4,797,368; International Patent Publication No.WO 93/24641; Kotin (1994) Human Gene Therapy 5:793-801; Muzyczka (1994)J. Clin. Invest. 94:1351. Construction of recombinant AAV vectors aredescribed in a number of publications, including U.S. Pat. No.5,173,414; Tratschin et al. (1985) Mol. Cell. Biol. 5:3251-3260;Tratschin, et al. (1984) Mol. Cell. Biol. 4:2072-2081; Hermonat &Muzyczka (1984) PNAS USA 81:6466-6470; and Samulski et al. (1989) J.Virol. 63:03822-3828.

At least six viral vector approaches are currently available for genetransfer in clinical trials, which utilize approaches that involvecomplementation of defective vectors by genes inserted into helper celllines to generate the transducing agent.

pLASN and MFG-S are examples of retroviral vectors that have been usedin clinical trials (Dunbar et al. (1995) Blood 85:3048-305; Kohn et al.(1995) Nat. Med. 1:1017-102; Malech et al. (1997) PNAS USA94(22):12133-12138). PA317/pLASN was the first therapeutic vector usedin a gene therapy trial. (Blaese et al. (1995) Science 270:475-480).Transduction efficiencies of 50% or greater have been observed for MFG-Spackaged vectors. (Ellem et al. (1997) Immunol Immunother. 44(1):10-20;Dranoff et al. (1997) Hum. Gene Ther. 1:111-2).

Recombinant adeno-associated virus vectors (rAAV) are a promisingalternative gene delivery systems based on the defective andnonpathogenic parvovirus adeno-associated type 2 virus. All vectors arederived from a plasmid that retains only the AAV 145 bp invertedterminal repeats flanking the transgene expression cassette. Efficientgene transfer and stable transgene delivery due to integration into thegenomes of the transduced cell are key features for this vector system.(Wagner et al. (1998) Lancet 351(9117):1702-3, Kearns et al. (1996) GeneTher. 9:748-55). Other AAV serotypes, including AAV1, AAV3, AAV4, AAV5,AAV6, AAV8, AAV8.2, AAV9 and AAVrh10 and pseudotyped AAV such as AAV2/8,AAV2/5 and AAV2/6 can also be used in accordance with the presentinvention.

Replication-deficient recombinant adenoviral vectors (Ad) can beproduced at high titer and readily infect a number of different celltypes. Most adenovirus vectors are engineered such that a transgenereplaces the Ad E1a, E1b, and/or E3 genes; subsequently the replicationdefective vector is propagated in human 293 cells that supply deletedgene function in trans. Ad vectors can transduce multiple types oftissues in vivo, including nondividing, differentiated cells such asthose found in liver, kidney and muscle. Conventional Ad vectors have alarge carrying capacity. An example of the use of an Ad vector in aclinical trial involved polynucleotide therapy for antitumorimmunization with intramuscular injection (Sterman et al. (1998) Hum.Gene Ther. 7:1083-9). Additional examples of the use of adenovirusvectors for gene transfer in clinical trials include Rosenecker et al.(1996) Infection 24(1):5-10; Sterman et al. (1998) Hum. Gene Ther.9(7):1083-1089; Welsh et al. (1995) Hum. Gene Ther. 2:205-18; Alvarez etal. (1997) Hum. Gene Ther. 5:597-613; Topf et al. (1998) Gene Ther.5:507-513; Sterman et al. (1998) Hum. Gene Ther. 7:1083-1089.

Packaging cells are used to form virus particles that are capable ofinfecting a host cell. Such cells include 293 cells, which packageadenovirus and AAV, and ψ2 cells or PA317 cells, which packageretrovirus. Viral vectors used in gene therapy are usually generated bya producer cell line that packages a nucleic acid vector into a viralparticle. The vectors typically contain the minimal viral sequencesrequired for packaging and subsequent integration into a host (ifapplicable), other viral sequences being replaced by an expressioncassette encoding the protein to be expressed. The missing viralfunctions are supplied in trans by the packaging cell line. For example,AAV vectors used in gene therapy typically only possess invertedterminal repeat (ITR) sequences from the AAV genome which are requiredfor packaging and integration into the host genome. Viral DNA ispackaged in a cell line, which contains a helper plasmid encoding theother AAV genes, namely rep and cap, but lacking ITR sequences. The cellline is also infected with adenovirus as a helper. The helper viruspromotes replication of the AAV vector and expression of AAV genes fromthe helper plasmid. The helper plasmid is not packaged in significantamounts due to a lack of ITR sequences. Contamination with adenoviruscan be reduced by, e.g., heat treatment to which adenovirus is moresensitive than AAV. In addition, AAV can be manufactured using abaculovirus system (see e.g. U.S. Pat. Nos. 6,723,551 and 7,271,002).

Purification of AAV particles from a 293 or baculovirus system typicallyinvolves growth of the cells which produce the virus, followed bycollection of the viral particles from the cell supernatant or lysingthe cells and collecting the virus from the crude lysate. AAV is thenpurified by methods known in the art including ion exchangechromatography (e.g. see U.S. Pat. Nos. 7,419,817 and 6,989,264), ionexchange chromatography and CsCl density centrifugation (e.g.International Patent Publication No. WO 2011/094198 A10), immunoaffinitychromatography (e.g. International Patent Publication No. WO2016/128408) or purification using AVB Sepharose (e.g. GE HealthcareLife Sciences).

In many gene therapy applications, it is desirable that the gene therapyvector be delivered with a high degree of specificity to a particulartissue type. Accordingly, a viral vector can be modified to havespecificity for a given cell type by expressing a ligand as a fusionprotein with a viral coat protein on the outer surface of the virus. Theligand is chosen to have affinity for a receptor known to be present onthe cell type of interest. For example, Han et al. (1995) Proc. Natl.Acad. Sci. USA 92:9747-9751, reported that Moloney murine leukemia viruscan be modified to express human heregulin fused to gp70, and therecombinant virus infects certain human breast cancer cells expressinghuman epidermal growth factor receptor. This principle can be extendedto other virus-target cell pairs, in which the target cell expresses areceptor and the virus expresses a fusion protein comprising a ligandfor the cell-surface receptor. For example, filamentous phage can beengineered to display antibody fragments (e.g., FAB or Fv) havingspecific binding affinity for virtually any chosen cellular receptor.Although the above description applies primarily to viral vectors, thesame principles can be applied to nonviral vectors. Such vectors can beengineered to contain specific uptake sequences which favor uptake byspecific target cells.

Gene therapy vectors can be delivered in vivo by administration to anindividual patient, typically by systemic administration (e.g.,intravenous, intraperitoneal, intramuscular, subdermal, or intracranialinfusion) or topical application, as described below. Alternatively,vectors can be delivered to cells ex vivo, such as cells explanted froman individual patient (e.g., lymphocytes, bone marrow aspirates, tissuebiopsy) or universal donor hematopoietic stem cells, followed byre-implantation of the cells into a patient, usually after selection forcells which have incorporated the vector.

Ex vivo cell transfection for diagnostics, research, transplant or forgene therapy (e.g., via re-infusion of the transfected cells into thehost organism) is well known to those of skill in the art. In apreferred embodiment, cells are isolated from the subject organism,transfected with a DNA-binding proteins nucleic acid (gene or cDNA), andre-infused back into the subject organism (e.g., patient). Various celltypes suitable for ex vivo transfection are well known to those of skillin the art (see, e.g., Freshney et al., Culture of Animal Cells, AManual of Basic Technique (3rd ed. 1994)) and the references citedtherein for a discussion of how to isolate and culture cells frompatients).

In one embodiment, stem cells are used in ex vivo procedures for celltransfection and gene therapy. The advantage to using stem cells is thatthey can be differentiated into other cell types in vitro, or can beintroduced into a mammal (such as the donor of the cells) where theywill engraft in the bone marrow. Methods for differentiating CD34+ cellsin vitro into clinically important immune cell types using cytokinessuch a GM-CSF, IFN-7 and TNF-α are known (see Inaba et al. (1992) J.Exp. Med. 176:1693-1702).

Stem cells are isolated for transduction and differentiation using knownmethods. For example, stem cells are isolated from bone marrow cells bypanning the bone marrow cells with antibodies which bind unwanted cells,such as CD4+ and CD8+ (T cells), CD45+ (panB cells), GR-1(granulocytes), and lad (differentiated antigen presenting cells) (seeInaba et al. (1992) J. Exp. Med. 176:1693-1702).

Stem cells that have been modified may also be used in some embodiments.For example, neuronal stem cells that have been made resistant toapoptosis may be used as therapeutic compositions where the stem cellsalso contain the ZFP TFs of the invention. Resistance to apoptosis maycome about, for example, by knocking out BAX and/or BAK using BAX- orBAK-specific ZFNs (see, U.S. Patent Publication No. 2010/0003756) in thestem cells, or those that are disrupted in a caspase, again usingcaspase-6 specific ZFNs for example. These cells can be transfected withthe ZFP TFs that are known to regulate TCR.

Vectors (e.g., retroviruses, adenoviruses, liposomes, etc.) containingtherapeutic DNA-binding proteins (or nucleic acids encoding theseproteins) can also be administered directly to an organism fortransduction of cells in vivo. Alternatively, naked DNA can beadministered. Administration is by any of the routes normally used forintroducing a molecule into ultimate contact with blood or tissue cellsincluding, but not limited to, injection, infusion, topical applicationand electroporation. Suitable methods of administering such nucleicacids are available and well known to those of skill in the art, and,although more than one route can be used to administer a particularcomposition, a particular route can often provide a more immediate andmore effective reaction than another route.

Methods for introduction of DNA into hematopoietic stem cells aredisclosed, for example, in U.S. Pat. No. 5,928,638. Vectors useful forintroduction of transgenes into hematopoietic stem cells, e.g., CD34+cells, include adenovirus Type 35.

Vectors suitable for introduction of transgenes into immune cells (e.g.,T-cells) include non-integrating lentivirus vectors. See, for example,Ory et al. (1996) Proc. Natl. Acad. Sci. USA 93:11382-11388; Dull et al.(1998) J. Virol. 72:8463-8471; Zuffery et al. (1998) J. Virol.72:9873-9880; Follenzi et al. (2000) Nature Genetics 25:217-222.

Pharmaceutically acceptable carriers are determined in part by theparticular composition being administered, as well as by the particularmethod used to administer the composition. Accordingly, there is a widevariety of suitable formulations of pharmaceutical compositionsavailable, as described below (see, e.g., Remington's PharmaceuticalSciences, 17th ed., 1989).

As noted above, the disclosed methods and compositions can be used inany type of cell including, but not limited to, prokaryotic cells,fungal cells, Archaeal cells, plant cells, insect cells, animal cells,vertebrate cells, mammalian cells and human cells, including T-cells andstem cells of any type. Suitable cell lines for protein expression areknown to those of skill in the art and include, but are not limited toCOS, CHO (e.g., CHO-S, CHO-K1, CHO-DG44, CHO-DUXB11), VERO, MDCK, WI38,V79, B14AF28-G3, BHK, HaK, NS0, SP2/0-Ag14, HeLa, HEK293 (e.g.,HEK293-F, HEK293-H, HEK293-T), perC6, insect cells such as Spodopterafrugiperda (Sf), and fungal cells such as Saccharomyces, Pichia andSchizosaccharomyces. Progeny, variants and derivatives of these celllines can also be used.

Applications

The disclosed compositions and methods can be used for any applicationin which it is desired to modulate B2M expression and/or functionality,including but not limited to, therapeutic and research applications inwhich B2M modulation is desirable. For example, the disclosedcompositions can be used in vivo and/or ex vivo (cell therapies) todisrupt the expression of endogenous B2M in T cells modified foradoptive cell therapy to express one or more exogenous CARs, exogenousTCRs, exogenous ACTR or other cancer-specific receptor molecules,thereby treating and/or preventing the cancer. In addition, in suchsettings, modulation of B2M expression within a cell can eliminate orsubstantially reduce the risk of an unwanted cross reaction withhealthy, nontargeted tissue (i.e. a graft-vs-host response).

Methods and compositions also include stem cell compositions wherein theB2M gene within the stem cells has been modulated (modified) and thecells further comprise an ACTR and/or a CAR and/or an isolated orengineered TCR. For example, B2M knock out or knock down modulatedallogeneic hematopoietic stem cells can be introduced into a HLAnon-matched patient following bone marrow ablation. These altered HSCwould allow the re-colonization of the patient but would not causepotential GvHD. The introduced cells may also have other alterations tohelp during subsequent therapy (e.g., chemotherapy resistance) to treatthe underlying disease. The HLA null cells also have use as an “off theshelf” therapy in emergency room situations with trauma patients.

The methods and compositions of the invention are also useful for thedesign and implementation of in vitro and in vivo models, for example,animal models of B2M and/or HLA and associated disorders, which allowsfor the study of these disorders.

All patents, patent applications and publications mentioned herein arehereby incorporated by reference in their entireties.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity and understanding,it will be apparent to those of skill in the art that various changesand modifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing disclosure andfollowing examples should not be construed as limiting.

EXAMPLES Example 1: Design of B2M-Specific Nucleases

B2M-specific ZFNs were constructed to enable site specific introductionof double strand breaks at the B2M gene. ZFNs were designed essentiallyas described in Urnov et al. (2005) Nature 435(7042):646-651, Lombardoet al. (2007) Nat Biotechnol. November; 25(11):1298-306, and U.S. PatentPublication Nos. 2008/0131962; 2015/0164954; 2014/0120622; and2014/0301990 and U.S. Pat. No. 8,956,828. The ZFN pairs targeteddifferent sites in the constant region of the B2M gene (see FIG. 1). Therecognition helices for exemplary ZFN pairs as well as the targetsequence are shown below in Table 1. Target sites of the B2M zinc-fingerdesigns are shown in the first column. Nucleotides in the target sitethat are targeted by the ZFP recognition helices are indicated inuppercase letters; non-targeted nucleotides indicated in lowercase.Linkers used to join the FokI nuclease domain and the ZFP DNA bindingdomain are also shown (see U.S. Patent Publication No. 2015/0132269).For example, the amino acid sequence of the domain linker LO is DNAbinding domain-QLVKS-FokI nuclease domain (SEQ ID NO:3). Similarly, theamino acid sequences for the domain linker N7a is FokI nucleasedomain-SGTPHEVGVYTL-DNA binding domain (SEQ ID NO:4), and N6a is FokInuclease domain-SGAQGSTLDF-DNA binding domain (SEQ ID NO:5).

TABLE 1 B2MZinc-fingerDesigns ZFN Name target Domain sequence F1 F2 F3F4 F5 F6 linker SBS57071 RSDDLSK DSSARKK DRSNLSR QRTHLRD QSGHLAR DSSNREAL0 5′ (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID gcCACGGA NO: 49)NO: 50) NO: 51) NO: 52) NO: 53) NO: 54) gCGAGACA TCTCGgcc cgaa (SEQ IDNO: 6) SBS57531 AQCCLFH DQSNLRA RSANLTR RSDDLTR QSGSLTR NA N6a 5′gaGTAG(SEQ (SEQ ID (SEQ ID (SEQ ID (SEQ ID CGcGAGCA ID NO: 56) NO: 57) NO: 58)NO: 59) CAGCtaag NO: 55) gccacg (SEQ ID NO: 7) SB557362 LNHHLQQ QSGNLARRSDTLSA QNAHRKT RSDNLSE KPYNLRT N6a 5′tcCAGC (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID (SEQ ID AGAGAATG NO: 60) NO: 61) NO: 62) NO: 63) NO: 64)NO: 65) GAAAGTca aatttc (SEQ ID NO: 8) SB557376 TRDHLST RSDARTN QSSDLSRHRSSLKN QSSHLTR DSSDRKK L0 5′ttTCCT (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID GAATTGCT NO: 66) NO: 67) NO: 68) NO: 69) NO: 70) NO: 71)ATGTGTct gggttt (SEQ ID NO: 9) SB557017 RSDNLSE ASKTRTN QSGNLAR TSGNLTRTSGNLTR RIQDLNK N7a 5′tgTCGG (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID ATgGATGA NO: 64) NO: 72) NO: 61) NO: 73) NO: 73) NO: 74)AACCCAGa cacata (SEQ ID NO: 10) SB557327 DRSNLSR ARWYLDK QSGNLAR AKWNLDAQQHVLQN QNATRTK L0 5′ (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ IDtaGCAATT NO: 51) NO: 75) NO: 61) NO: 76) NO: 77) NO: 78) CAGGAAaTTTGACttt ccat (SEQ ID NO: 11) SB557328 TNQSLHW QSGNLAR RSDNLRE ASHVLNAQNATRTK NA L0 5′taGCAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID TTCAGGAANO: 79) NO: 61) NO: 80) NO: 81) NO: 78) ATTtgact ttccat (SEQ ID NO: 11)SB557332 RSDNLSE ASKTRTN QSGNLAR TSANLSR TSGNLTR RTEDRLA N6a 5′tgTCGG(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID ATgGATGA NO: 64) NO: 72)NO: 61) NO: 82) NO: 73) NO: 83) AACCCAGa cacata (SEQ ID NO: 10) SB557469RSDNLSE ASKTRTN YTSSLCY QSGHLSR TSGNLTR RIQDLNK N7a 5′tgTCGG (SEQ ID(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID ATGGATGA NO: 64) NO: 72) NO: 84)NO: 85) NO: 73) NO: 74) aACCCAGa cacata (SEQ ID NO: 10) SBS57331 RSDNLSEASKTRKN QSGNLAR TSANLSR TSGNLTR RIQDLNK N6a 5′tgTCGG (SEQ ID (SEQ ID(SEQ ID (SEQ ID (SEQ ID (SEQ ID ATgGATGA NO: 64) NO: 86) NO: 61) NO: 82)NO: 73) NO: 74) AACCCAGa cacata (SEQ ID NO: 10) SB557326 DRSNLSR ARWYLDKQSGNLAR AKWNLDA TTPVLVQ QNATRTK LO 5′taGCAA (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID (SEQ ID TTCAGGAA NO: 51) NO: 75) NO: 61) NO: 76) NO: 87)NO: 78) aTTTGACt ttccat (SEQ ID NO: 11) SB555822 DRSNLSR FPGSRTR QSGNLARWRISLAA DRSNLSR DSSDRKK N7a 5′caTCCG (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID (SEQ ID ACATTGAA NO: 51) NO: 88) NO: 61) NO: 89) NO: 51) NO: 71)GTTGACtt actgaa (SEQ ID NO: 12) SB557511 DQSLLRT QSGNLAR HRLGLRD RSANLTRRSDVLST QNAHRIK L0 5′gaAGAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID TGGAGAGA NO: 90) NO: 61) NO: 91) NO: 57) NO: 92) NO: 93)GAATTGaa aaagtg (SEQ ID NO: 13) SB557509 DQSLLRT QSGNLAR QSAHRKN RSANLTRRSDVLST QNAHRIK L0 5′gaAGAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID TGGAGAGA NO: 90) NO: 61) NO: 94) NO: 57) NO: 92) NO: 93)GAATTGaa aaagtg (SEQ ID NO: 13) SB557482 DRSNLSR FPGSRTR QSGNLAR HKLSLSIDSSDRKK N7a 5′caTCCG (SEQ ID (SEQ ID (SEQ ID (SEQ ID DRSNLSR (SEQ IDACATTGAA NO: 51) NO: 88) NO: 61) NO: 95) (SEQ ID NO: 71) GTTGACttNO: 51) actgaa (SEQ ID NO: 12) SB557347 DQSLLRT QSGNLAR QNAHRKT RSANLTRRSDVLST QNAHRIK L0 5′gaAGAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID(SEQ ID TGGAGAGA NO: 90) NO: 61) NO: 63) NO: 57) NO: 92) NO: 93)GAATTGaa aaagtg (SEQ ID NO: 13) SB557296 RSANLTR QSAHRKN RHSHLTS QSGNLARQSNQLAV NA N7a 5′ctGAAG (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID AATGGAGANO: 57) NO: 94) NO: 96) NO: 61) NO: 97) GAGaattg aaaaag (SEQ ID NO: 14)SB557322 DRSNLSR QSADRTK TNQNRIT RSANLTR RSDSLSV QNANRKT L0 5′aaAAAG(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID TGGAGCAT NO: 51) NO: 98)NO: 99) NO: 57) NO: 100) NO: 101) TCAGACtt gtcttt (SEQ ID NO: 15)SB557323 DRSNLSR QSADRTK LKQNLDA RSANLTR RSDSLSV QNANRKT L0 5′ (SEQ ID(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID aaAAAGTG NO: 51) NO: 98)NO: 103) NO: 57) NO: 100) NO: 101) GAGCATTC AGACttgt cttt (SEQ IDNO: 15) SB557447 RSANLTR QSAHRKN RHSHLTS QSGNLAR QRGNLWT NA N7a 5′ctGAAG(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID AATGGAGA NO: 57) NO: 94) NO: 96)NO: 61) NO: 102) GAGaattg aaaaag (SEQ ID NO: 14)

All ZFNs were tested and found to bind to their target sites and foundto be active as nucleases.

Guide RNAs for the S. pyogenes CRISPR/Cas9 system were also constructedto target the B2M gene. The target sequences in the B2M gene areindicated as well as the guide RNA sequences in Table 2A below. Allguide RNAs are tested in the CRISPR/Cas9 system and are found to beactive. The lowercase “g” at the 5′ end of some of the guide sequencesindicates an added G nucleotide to serve in the PAM sequence.

TABLE 2A Guide RNAs for the constant region of human B2M Name StrandTarget (5′ → 3′) gRNA (5′ → 3′) B2M- f GGCCGAGATGTCTCGCTCCGTGGGGCCGAGATGTCTCGCTCCG Gf1073 (SEQ ID NO: 16) (SEQ ID NO: 104) B2M- rCGCGAGCACAGCTAAGGCCACGG gCGCGAGCACAGCTAAGGCCA Gr1074 (SEQ ID NO: 17)(SEQ ID NO: 105) B2M- r GAGTAGCGCGAGCACAGCTAAGG GAGTAGCGCGAGCACAGCTAGr1080 (SEQ ID NO: 18) (SEQ ID NO: 106) B2M- f CTCGCGCTACTCTCTCTTTCTGGgCTCGCGCTACTCTCTCTTTC Gf1107 (SEQ ID NO: 19) (SEQ ID NO: 107) B2M- fGCTACTCTCTCTTTCTGGCCTGG GCTACTCTCTCTTTCTGGCC Gf1112 (SEQ ID NO: 20)(SEQ ID NO: 108) B2M- f ACTCTCTCTTTCTGGCCTGGAGG gACTCTCTCTTTCTGGCCTGGGf1115 (SEQ ID NO: 21) (SEQ ID NO: 109) B2M- r ACTCACGCTGGATAGCCTCCAGGgACTCACGCTGGATAGCCTCC Gr1114 (SEQ ID NO: 22) (SEQ ID NO: 110) B2M- rAGGGTAGGAGAGACTCACGCTGG gAGGGTAGGAGAGACTCACGC Gr1126 (SEQ ID NO: 23)(SEQ ID NO: 111) B2M- r CGTGAGTAAACCTGAATCTTTGG gCGTGAGTAAACCTGAATCTTGr4942 (SEQ ID NO: 24) (SEQ ID NO: 112) B2M- f CTCAGGTACTCCAAAGATTCAGGgCTCAGGTACTCCAAAGATTC Gf4948 (SEQ ID NO: 25) (SEQ ID NO: 113) B2M- rTTTGACTTTCCATTCTCTGCTGG gTTTGACTTTCCATTCTCTGC Gr4969 (SEQ ID NO: 26)(SEQ ID NO: 114) B2M- f TCACGTCATCCAGCAGAGAATGG gTCACGTCATCCAGCAGAGAAGf4976 (SEQ ID NO: 27) (SEQ ID NO: 115) B2M- r ACCCAGACACATAGCAATTCAGGgACCCAGACACATAGCAATTC Gr4995 (SEQ ID NO: 28) (SEQ ID NO: 116) B2M- fTTCCTGAATTGCTATGTGTCTGG gTTCCTGAATTGCTATGTGTC Gf5009 (SEQ ID NO: 29)(SEQ ID NO: 117) B2M- f TCCTGAATTGCTATGTGTCTGGG gTCCTGAATTGCTATGTGTCTGf5010 (SEQ ID NO: 30) (SEQ ID NO: 118) B2M- r AAGTCAACTTCAATGTCGGATGGgAAGTCAACTTCAATGTCGGA Gr5023 (SEQ ID NO: 31) (SEQ ID NO: 119) B2M- rCAGTAAGTCAACTTCAATGTCGG gCAGTAAGTCAACTTCAATGT Gr5027 (SEQ ID NO: 32)(SEQ ID NO: 120) B2M- f GAAGTTGACTTACTGAAGAATGG GAAGTTGACTTACTGAAGAAGf5051 (SEQ ID NO: 33) (SEQ ID NO: 121) B2M- f TGGAGAGAGAATTGAAAAAGTGGgTGGAGAGAGAATTGAAAAAG Gf5071 (SEQ ID NO: 34) (SEQ ID NO: 122) B2M- fTTCAGACTTGTCTTTCAGCAAGG gTTCAGACTTGTCTTTCAGCA Gf5098 (SEQ ID NO: 35)(SEQ ID NO: 123) B2M- f ACTTGTCTTTCAGCAAGGACTGG gACTTGTCTTTCAGCAAGGACGf5103 (SEQ ID NO: 36) (SEQ ID NO: 124) B2M- r ATACTCATCTTTTTCAGTGGGGGgATACTCATCTTTTTCAGTGG Gr5141 (SEQ ID NO: 37) (SEQ ID NO: 125) B2M- rCATACTCATCTTTTTCAGTGGGG gCATACTCATCTTTTTCAGTG Gr5142 (SEQ ID NO: 38)(SEQ ID NO: 126) B2M- r GCATACTCATCTTTTTCAGTGGG GCATACTCATCTTTTTCAGTGr5143 (SEQ ID NO: 39) (SEQ ID NO: 127) B2M- r GGCATACTCATCTTTTTCAGTGGGGCATACTCATCTTTTTCAG Gr5144 (SEQ ID NO: 40) (SEQ ID NO: 128) B2M- rAGTCACATGGTTCACACGGCAGG gAGTCACATGGTTCACACGGC Gr5165 (SEQ ID NO: 41)(SEQ ID NO: 129) B2M- r ACAAAGTCACATGGTTCACACGG gACAAAGTCACATGGTTCACAGr5169 (SEQ ID NO: 42) (SEQ ID NO: 130) B2M- r TGGGCTGTGACAAAGTCACATGGgTGGGCTGTGACAAAGTCACA Gr5178 (SEQ ID NO: 43) (SEQ ID NO: 131) B2M- rTTACCCCACTTAACTATCTTGGG gTTACCCCACTTAACTATCTT Gr5197 (SEQ ID NO: 44)(SEQ ID NO: 132) B2M- r CTTACCCCACTTAACTATCTTGG gCTTACCCCACTTAACTATCTGr5198 (SEQ ID NO: 45) (SEQ ID NO: 133) B2M- f CACAGCCCAAGATAGTTAAGTGGgCACAGCCCAAGATAGTTAAG Gf5208 (SEQ ID NO: 46) (SEQ ID NO: 134) B2M- fACAGCCCAAGATAGTTAAGTGGG gACAGCCCAAGATAGTTAAGT Gf5209 (SEQ ID NO: 47)(SEQ ID NO: 135) B2M- f CAGCCCAAGATAGTTAAGTGGGG gCAGCCCAAGATAGTTAAGTGGf5210 (SEQ ID NO: 48) (SEQ ID NO: 136)

TALENs were made to target the B2M locus and are shown below in Table2B. All TALENs were tested in K562 cells and found to be active (seeTable 2C and FIG. 2B).

TABLE 2B TALENs specific for B2M SBS # Target site 5′ → 3′ RVDs N → C103049 atTCGGGCCGAGATGTCTCgcNG-HD-NN-NN-NN-HD-HD-NN-NI-NN-NI-NG-NN-NG-HD-NG- (SEQ ID NO: 137) HD103050 gtAGCGCGAGCACAGCTAAggNI-NN-HD-NN-HD-NN-NI-NN-HD-NI-HD-NI-NN-HD-NG-NI-NI (SEQ ID NO: 138)103051 ctCCGTGGCCTTAGCTGTGctHD-HD-NN-NG-NN-NN-HD-HD-NG-NG-NI-NN-HD-NG-NN-NG- (SEQ ID NO: 139) NK103052 ctCCAGGCCAGAAAGAGAGagHD-HD-NI-NN-NN-HD-HD-NI-NN-NI-NI-NI-NN-NI-NN-NI-NK (SEQ ID NO: 140)103053 gtGGCCTTAGCTGTGCTCGcgNN-NN-HD-HD-NG-NG-NI-NN-HD-NG-NN-NG-NN-HD-NG-HD- (SEQ ID NO: 141) NK103054 atAGCCTCCAGGCCAGAAAgaNI-NN-HD-HD-NG-HD-HD-NI-NN-NN-HD-HD-NI-NN-NI-NI-NI (SEQ ID NO: 142)103055 ctTAGCTGTGCTCGCGCTActNG-NI-NN-HD-NG-NN-NG-NN-HD-NG-HD-NN-HD-NN-HD-NG- (SEQ ID NO: 143) NI103056 ctGGATAGCCTCCAGGCCAgaNN-NN-NI-NG-NI-NN-HD-HD-NG-HD-HD-NI-NN-NN-HD-HD- (SEQ ID NO: 144) NI103057 ctGTGCTCGCGCTACTCTCtcNN-NG-NN-HD-NG-HD-NN-HD-NN-HD-NG-NI-HD-NG-HD-NG- (SEQ ID NO: 145) HD103058 ctCACGCTGGATAGCCTCCagHD-NI-HD-NN-HD-NG-NN-NN-NI-NG-NI-NN-HD-HD-NG-HD- (SEQ ID NO: 146) HD103059 ctACTCTCTCTTTCTGGCCtgNI-HD-NG-HD-NG-HD-NG-HD-NG-NG-NG-HD-NG-NN-NN- (SEQ ID NO: 147) HD-HD103060 gtAGGAGAGACTCACGCTGgaNI-NN-NN-NI-NN-NI-NN-NI-HD-NG-HD-NI-HD-NN-HD-NG-NK (SEQ ID NO: 148)103061 gtGTCTTTTCCCGATATTCctNN-NG-HD-NG-NG-NG-NG-HD-HD-HD-NN-NI-NG-NI-NG-NG- (SEQ ID NO: 149) HD103062 gtGAGTAAACCTGAATCTTtgNN-NI-NN-NG-NI-NI-NI-HD-HD-NG-NN-NI-NI-NG-HD-NG-NG (SEQ ID NO: 150)103063 ttTTCCCGATATTCCTCAGgtNG-NG-HD-HD-HD-NN-NI-NG-NI-NG-NG-HD-HD-NG-HD-NI- (SEQ ID NO: 151) NK103064 atGACGTGAGTAAACCTGAatNN-NI-HD-NN-NG-NN-NI-NN-NG-NI-NI-NI-HD-HD-NG-NN-NI (SEQ ID NO: 152)103065 ttCCTCAGGTACTCCAAAGatHD-HD-NG-HD-NI-NN-NN-NG-NI-HD-NG-HD-HD-NI-NI-NI-NK (SEQ ID NO: 153)103066 ctCTGCTGGATGACGTGAGtaHD-NG-NN-HD-NG-NN-NN-NI-NG-NN-NI-HD-NN-NG-NN-NI- (SEQ ID NO: 154) NK103067 ctCAGGTACTCCAAAGATTcaHD-NI-NN-NN-NG-NI-HD-NG-HD-HD-NI-NI-NI-NN-NI-NG-NG (SEQ ID NO: 155)103068 atTCTCTGCTGGATGACGTgaNG-HD-NG-HD-NG-NN-HD-NG-NN-NN-NI-NG-NN-NI-HD-NN- (SEQ ID NO: 156) NG103069 gtACTCCAAAGATTCAGGTttNI-HD-NG-HD-HD-NI-NI-NI-NN-NI-NG-NG-HD-NI-NN-NN-NG (SEQ ID NO: 157)103070 ttTCCATTCTCTGCTGGATgaNG-HD-HD-NI-NG-NG-HD-NG-HD-NG-NN-HD-NG-NN-NN-NI- (SEQ ID NO: 158) NG103071 ctCCAAAGATTCAGGTTTActHD-HD-NI-NI-NI-NN-NI-NG-NG-HD-NI-NN-NN-NG-NG-NG-NI (SEQ ID NO: 159)103072 ttGACTTTCCATTCTCTGCtgNN-NI-HD-NG-NG-NG-HD-HD-NI-NG-NG-HD-NG-HD-NG-NN- (SEQ ID NO: 160) HD103073 ctCACGTCATCCAGCAGAGaaHD-NI-HD-NN-NG-HD-NI-NG-HD-HD-NI-NN-HD-NI-NN-NI-NK (SEQ ID NO: 161)103074 atAGCAATTCAGGAAATTTgaNI-NN-HD-NI-NI-NG-NG-HD-NI-NN-NN-NI-NI-NI-NG-NG-NG (SEQ ID NO: 162)103075 ttCCTGAATTGCTATGTGTctHD-HD-NG-NN-NI-NI-NG-NG-NN-HD-NG-NI-NG-NN-NG-NN- (SEQ ID NO: 163) NG103076 gtCAACTTCAATGTCGGATggHD-NI-NI-HD-NG-NG-HD-NI-NI-NG-NN-NG-HD-NN-NN-NI-NG (SEQ ID NO: 164)103077 ctATGTGTCTGGGTTTCATccNI-NG-NN-NG-NN-NG-HD-NG-NN-NN-NN-NG-NG-NG-HD-NI- (SEQ ID NO: 165) NG103078 ttCTTCAGTAAGTCAACTTcaHD-NG-NG-HD-NI-NN-NG-NI-NI-NN-NG-HD-NI-NI-HD-NG-NG (SEQ ID NO: 166)103079 atGTGTCTGGGTTTCATCCatNN-NG-NN-NG-HD-NG-NN-NN-NN-NG-NG-NG-HD-NI-NG-HD- (SEQ ID NO: 167) HD103080 atTCTTCAGTAAGTCAACTtcNG-HD-NG-NG-HD-NI-NN-NG-NI-NI-NN-NG-HD-NI-NI-HD-NG (SEQ ID NO: 168)103081 gtCTGGGTTTCATCCATCCgaHD-NG-NN-NN-NN-NG-NG-NG-HD-NI-NG-HD-HD-NI-NG-HD- (SEQ ID NO: 169) HD103082 ctCCATTCTTCAGTAAGTCaaHD-HD-NI-NG-NG-HD-NG-NG-HD-NI-NN-NG-NI-NI-NN-NG- (SEQ ID NO: 170) HD103083 ttTCATCCATCCGACATTGaaNG-HD-NI-NG-HD-HD-NI-NG-HD-HD-NN-NI-HD-NI-NG-NG- (SEQ ID NO: 171) NK103084 ttCTCTCTCCATTCTTCAGtaHD-NG-HD-NG-HD-NG-HD-HD-NI-NG-NG-HD-NG-NG-HD-NI- (SEQ ID NO: 172) NK103085 atCCATCCGACATTGAAGTtgHD-HD-NI-NG-HD-HD-NN-NI-HD-NI-NG-NG-NN-NI-NI-NN-NG (SEQ ID NO: 173)103086 ttCAATTCTCTCTCCATTCttHD-NI-NI-NG-NG-HD-NG-HD-NG-HD-NG-HD-HD-NI-NG-NG- (SEQ ID NO: 174) HD103087 atCCGACATTGAAGTTGACttHD-HD-NN-NI-HD-NI-NG-NG-NN-NI-NI-NN-NG-NG-NN-NI-HD (SEQ ID NO: 175)103088 ctTTTTCAATTCTCTCTCCatNG-NG-NG-NG-HD-NI-NI-NG-NG-HD-NG-HD-NG-HD-NG-HD- (SEQ ID NO: 176) HD103089 ttGAAGTTGACTTACTGAAgaNN-NI-NI-NN-NG-NG-NN-NI-HD-NG-NG-NI-HD-NG-NN-NI-NI (SEQ ID NO: 177)103090 atGCTCCACTTTTTCAATTctNN-HD-NG-HD-HD-NI-HD-NG-NG-NG-NG-NG-HD-NI-NI-NG- (SEQ ID NO: 178) NG103091 gtTGACTTACTGAAGAATGgaNG-NN-NI-HD-NG-NG-NI-HD-NG-NN-NI-NI-NN-NI-NI-NG-NK (SEQ ID NO: 179)103092 gtCTGAATGCTCCACTTTTtcHD-NG-NN-NI-NI-NG-NN-HD-NG-HD-HD-NI-HD-NG-NG-NG- (SEQ ID NO: 180) NG103093 atGGAGAGAGAATTGAAAAag NN-NN-NI-NN-NI-NN-NI-NN-NI-NI-NG-NG-NN-NI-NI-NI-NI (SEQ ID NO: 181)103094 ctTGCTGAAAGACAAGTCTgaNG-NN-HD-NG-NN-NI-NI-NI-NN-NI-HD-NI-NI-NN-NG-HD-NG (SEQ ID NO: 182)103095 ttCAGACTTGTCTTTCAGCaaHD-NI-NN-NI-HD-NG-NG-NN-NG-HD-NG-NG-NG-HD-NI-NN- (SEQ ID NO: 183) HD103096 gtGTAGTACAAGAGATAGAaaNN-NG-NI-NN-NG-NI-HD-NI-NI-NN-NI-NN-NI-NG-NI-NN-NI (SEQ ID NO: 184)103097 ctTGTCTTTCAGCAAGGACtgNG-NN-NG-HD-NG-NG-NG-HD-NI-NN-HD-NI-NI-NN-NN-NI- (SEQ ID NO: 185) HD103098 atTCAGTGTAGTACAAGAGatNG-HD-NI-NN-NG-NN-NG-NI-NN-NG-NI-HD-NI-NI-NN-NI-NK (SEQ ID NO: 186)103099 ctTTCAGCAAGGACTGGTCttNG-NG-HD-NI-NN-HD-NI-NI-NN-NN-NI-HD-NG-NN-NN-NG- (SEQ ID NO: 187) HD103100 gtGAATTCAGTGTAGTACAagNN-NI-NI-NG-NG-HD-NI-NN-NG-NN-NG-NI-NN-NG-NI-HD-NI (SEQ ID NO: 188)103101 ctGGTCTTTCTATCTCTTGtaNN-NN-NG-HD-NG-NG-NG-HD-NG-NI-NG-HD-NG-HD-NG-NG- (SEQ ID NO: 189) NK103102 ttTTTCAGTGGGGGTGAATtcNG-NG-NG-HD-NI-NN-NG-NN-NN-NN-NN-NN-NG-NN-NI-NI- (SEQ ID NO: 190) NG103103 ctATCTCTTGTACTACACTgaNI-NG-HD-NG-HD-NG-NG-NN-NG-NI-HD-NG-NI-HD-NI-HD- (SEQ ID NO: 191) NG103104 atACTCATCTTTTTCAGTGggNI-HD-NG-HD-NI-NG-HD-NG-NG-NG-NG-NG-HD-NI-NN-NG- (SEQ ID NO: 192) NK103105 ctACACTGAATTCACCCCCacNI-HD-NI-HD-NG-NN-NI-NI-NG-NG-HD-NI-HD-HD-HD-HD- (SEQ ID NO: 193) HD103106 ttCACACGGCAGGCATACTcaHD-NI-HD-NI-HD-NN-NN-HD-NI-NN-NN-HD-NI-NG-NI-HD-NG (SEQ ID NO: 194)103107 atTCACCCCCACTGAAAAAgaNG-HD-NI-HD-HD-HD-HD-HD-NI-HD-NG-NN-NI-NI-NI-NI-NI (SEQ ID NO: 195)103108 gtCACATGGTTCACACGGCagHD-NI-HD-NI-NG-NN-NN-NG-NG-HD-NI-HD-NI-HD-NN-NN- (SEQ ID NO: 196) HD103109 atTCACCCCCACTGAAAAAgaNG-HD-NI-HD-HD-HD-HD-HD-NI-HD-NG-NN-NI-NI-NI-NI-NI (SEQ ID NO: 195)103110 gtCACATGGTTCACACGGCagHD-NI-HD-NI-NG-NN-NN-NG-NG-HD-NI-HD-NI-HD-NN-NN- (SEQ ID NO: 196) HD103111 ctGAAAAAGATGAGTATGCctNN-NI-NI-NI-NI-NI-NN-NI-NG-NN-NI-NN-NG-NI-NG-NN-HD (SEQ ID NO: 197)103112 ctGTGACAAAGTCACATGGttNN-NG-NN-NI-HD-NI-NI-NI-NN-NG-HD-NI-HD-NI-NG-NN-NK (SEQ ID NO: 198)103113 atGAGTATGCCTGCCGTGTgaNN-NI-NN-NG-NI-NG-NN-HD-HD-NG-NN-HD-HD-NN-NG-NN- (SEQ ID NO: 199) NG103114 ctATCTTGGGCTGTGACAAagNI-NG-HD-NG-NG-NN-NN-NN-HD-NG-NN-NG-NN-NI-HD-NI- (SEQ ID NO: 200) NI103115 gtATGCCTGCCGTGTGAACcaNI-NG-NN-HD-HD-NG-NN-HD-HD-NN-NG-NN-NG-NN-NI-NI- (SEQ ID NO: 201) HD103116 ttAACTATCTTGGGCTGTGacNI-NI-HD-NG-NI-NG-HD-NG-NG-NN-NN-NN-HD-NG-NN-NG- (SEQ ID NO: 202) NK103117 gtGTGAACCATGTGACTTTgtNN-NG-NN-NI-NI-HD-HD-NI-NG-NN-NG-NN-NI-HD-NG-NG- (SEQ ID NO: 203) NG103118 ttACCCCACTTAACTATCTtgNI-HD-HD-HD-HD-NI-HD-NG-NG-NI-NI-HD-NG-NI-NG-HD-NG (SEQ ID NO: 204)103119 atGTGACTTTGTCACAGCCcaNN-NG-NN-NI-HD-NG-NG-NG-NN-NG-HD-NI-HD-NI-NN-HD- (SEQ ID NO: 205) HD

The TALENs from Table 2B were tested at three different concentrationsof either 25, 100 or 400 ng of each TALEN per reaction. All TALENstested were found to bind to their target sites and were found to beactive as nucleases; exemplary data is shown in Table 2C and FIG. 2B.

TABLE 2C Activity of TALEN pairs in K562 cells SBS# % Indel-25 ng %Indel-100 ng % Indel-400 ng 103049:103050 2.0 7.3 19.5 103051:10305218.3 38.7 63.8 103053:103054 12.0 17.4 32.4 103055:103056 6.3 12.7 25.1103057:103058 15.7 24.5 46.2 103061:103062 3.1 5.7 22.9 103063:1030641.9 4.0 14.8 103065:103066 7.8 13.7 41.2 103067:103068 14.1 25.6 49.3103069:103070 2.4 5.0 27.9 103071:103072 1.5 3.6 13.3 103073:103074 0.10.5 3.0 103075:103076 0.3 0.5 1.5 103077:103078 2.0 5.8 17.1103079:103080 15.3 30.1 42.3 103081:103082 5.2 16.2 27.5 103083:1030847.3 12.2 32.2 103085:103086 0.3 1.3 3.9 103087:103088 0.7 4.4 10.5103089:103090 1.3 8.7 16.1 103091:103092 14.3 33.5 48.5 103093:1030942.4 7.6 20.2 103095:103096 12.0 23.5 42.0 103097:103098 10.0 28.3 52.0103099:103100 1.9 7.5 15.3 103101:103102 3.3 7.0 15.5 103103:103104 15.829.3 44.9 103105:103106 2.2 5.9 14.2 103107:103108 1.0 2.1 4.2103109:103110 1.0 3.8 8.0 103111:103112 11.3 30.2 26.5 103113:10311413.5 22.2 26.6 103115:103116 29.8 41.0 66.1 103117:103118 5.8 20.6 45.7103119:103120 14.5 40.9 57.7

Thus, the nucleases described herein (e.g., nucleases comprising a ZFP,a TALE or a sgRNA DNA-binding domain) bind to their target sites andcleave the B2M gene, thereby making genetic modifications within a B2Mgene comprising any of SEQ ID NO:6-48 or 137-205, includingmodifications (insertions and/or deletions) within any of thesesequences (SEQ ID NO:6-48 or 137-205); modifications within 1-50 (e.g.,1 to 10) base pairs of these gene sequences; modifications betweentarget sites of paired target sites (for dimers); and/or modificationswithin one or more of the following sequences: GGCCTTA, TCAAATT, TCAAAT,TTACTGA and/or AATTGAA (see, FIG. 1).

Furthermore, the DNA-binding domains (ZFPs, TALEs and sgRNAs) all boundto their target sites and are also formulated into active engineeredtranscription factors when associated with one or more transcriptionalregulatory domains.

Example 2: B2M-Specific ZFN Activity in T Cells

The B2M-specific ZFN pairs were tested in human T cells for nucleaseactivity. mRNAs encoding the ZFNs were transfected into purified Tcells. Briefly, T cells were obtained from leukopheresis product andpurified using the Miltenyi CliniMACS system (CD4 and CD8 dualselection). These cells were then activated using Dynabeads(ThermoFisher) according to manufacturer's protocol. 3 days postactivation, the cells were transfected with two doses of mRNA (2 or 6 μgin total of the two ZFNs) using a BTX 96 well electroporator (BTX)according to standard protocols. Cells were then expanded for anadditional 7 days for a total of 10 days following activation. Cellswere removed at day 7 and analyzed for on target B2M modification usingdeep sequencing (Miseq, Illumina) and at day 10 for FACs analysis usingHLA-A, -B and -C staining.

The B2M-specific ZFN pairs were all active in T cells and caused anaverage of 89% and 83% for the 6 μg and 2 μg mRNA doses respectively(see FIG. 2). The pairs used and the locations (shown in FIG. 1) arelisted below in Table 3.

TABLE 3 B2M specific ZFN pairs and target sites SBS Pair Site, pair57071 and 57531 A1 57362 and 57376 C1 57017 and 57327 D1 57017 and 57328D2 57332 and 57327 D3 57469 and 57327 D4 57469 and 57328 D5 57331 and57326 D6 55822 and 57511 E1 55822 and 57509 E2 57482 and 57511 E3 55822and 57347 E4 57296 and 57322 G1 57296 and 57323 G2 57447 and 57322 G3

Similarly, T cells treated with the ZFNs lost expression of HLA A, B andC, where FACS analysis showed an average of 81% and 67% HLA negative Tcells at the 6 μg and 2 μg mRNA doses respectively (see FIG. 3).

Example 3: Activity of Guide RNAs Against B2M In Vitro

In these experiments, Cas9 was supplied on a pVAX plasmid, and the sgRNAwas supplied on a plasmid under the control of the U6 promoter. Theplasmids were mixed at either 100 ng of each or 400 ng of each and weremixed with 2e5 cells per run. The cells were transfected using the Amaxasystem. Briefly, an Amaxa transfection kit was used and the nucleicacids were transfected using a standard Amaxa shuttle protocol.Following transfection, the cells were left to rest for 10 minutes atroom temperature and then resuspended in prewarmed RPMI. The cells werethen grown in standard conditions at 37′° C. Genomic DNA was isolated 7days after transfection and subject to MiSeq analysis.

The data shown below (Table 4) indicates the percent of indels(insertions and deletions) detected at the two doses of guide RNAs, andindicated that the different guide RNAs induced cleavage at the targetedsite. The numbers represent the average of two experiments. All guideswere active.

TABLE 4 Activity of CRISPR/Cas system on B2M ave 100 ng ave 400 ng GFPGuide (% indels) (% indels) (% indels) B2M-Gf1073 31.12 55.85 0.20B2M-Gr1074 35.21 55.86 0.24 B2M-Gr1080 24.83 62.22 0.17 B2M-Gf1107 4.3252.68 0.19 B2M-Gf1112 9.99 22.09 0.11 B2M-Gf1115 26.52 28.97 0.16B2M-Gr1114 16.93 53.88 0.12 B2M-Gr1126 15.25 55.92 0.04 B2M-Gr4942 3.0548.28 0.15 B2M-Gf4948 1.62 12.18 0.11 B2M-Gr4969 1.68 10.11 0.16B2M-Gf4976 7.47 12.65 0.14 B2M-Gr4995 1.14 31.89 0.16 B2M-Gf5009 0.938.87 0.10 B2M-Gf5010 0.30 5.84 0.16 B2M-Gr5023 2.66 2.41 0.22 B2M-Gr502714.90 13.13 0.19 B2M-Gf5051 12.98 42.24 0.25 B2M-Gf5071 5.16 47.59 0.44B2M-Gf5098 4.17 25.60 0.35 B2M-Gf5103 4.00 24.85 0.45 B2M-Gr5141 3.5318.55 0.32 B2M-Gr5142 3.26 18.22 0.35 B2M-Gr5143 1.79 20.51 0.35B2M-Gr5144 7.04 6.99 0.34 B2M-Gr5165 6.48 26.44 0.56 B2M-Gr5169 4.6234.59 0.44 B2M-Gr5178 3.62 30.98 0.61 B2M-Gr5197 2.32 23.26 0.52B2M-Gr5198 1.87 20.26 0.53 B2M-Gf5208 6.20 17.64 0.55 B2M-Gf5209 10.0935.92 0.17 B2M-Gf5210 8.47 21.72 0.21

Example 4: Double Knockout of B2M and TCR in Primary T Cells

The B2M pairs described herein were also tested in combination with ZFNspecific for TCRA (see Table 5 below and U.S. Patent Publication No.2017/0211075). The cells were obtained and treated as described inExample 2. mRNA encoding the ZFN pairs (SBS #57017/SBS #57327 for B2Mand SBS #55254/SBS #55248 for TCRA) were electroporated into the cellsusing a Maxcyte instrument according to manufacturer's instructions. Inbrief, the T cells were activated at day 0, and treated with theZFN-encoding mRNA on day 3 where the cell density was 3e7 cells/mL.Electroporation was followed by a 30° C. cold shock overnightpost-electroporation. On day 4, the cells were counted and assayed forviability, diluted to 0.5e6 cells/mL and the transferred to 37° C. Onday 7, the cells were counted and assayed again, and re-diluted to 0.5e6cells/mL. On days 10 and 14, portions of the cells were harvested forFACS and MiSeq deep sequencing analysis.

TABLE 5 TCRA ZFNs ZFN Name target Domain sequence F1 F2 F3 F4 F5 F6linker SB555266 QSSDLSR QSGNRTT RSANLAR DRSALAR RSDVLSE KHSTRRV N7c5′tcAAGCTGG (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID TCGAGaAAAGCNO: 68) NO: 208) NO: 209) NO: 210) NO: 211) NO: 212) Tttgaaac (SEQ IDNO: 206) SB553853 TMHQRVE TSGHLSR RSDHLTQ DSANLSR QSGSLTR AKWNLDA L05′aaCAGGTAa (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID GACAGGGGTCTNO: 213) NO: 214) NO: 215) NO: 216) NO: 59) NO: 76) Agcctggg (SEQ IDNO: 207) SB555254 RSDHLST DRSHLAR LKQHLNE QSGNLAR HNSSLKD N/A L05′ctCCTGAAA (SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID GTGGCCGGgtt NO: 219)NO: 220) NO: 221) NO: 61) NO: 222) taatctgc (SEQ ID NO: 217) S5B555248DQSNLRA TSSNRKT LQQTLAD QSGNLAR RREDLIT TSSNLSR L0 5′agGATTCGG (SEQ ID(SEQ ID (SEQ ID (SEQ ID (SEQ ID (SEQ ID AACCCAATCAC NO: 56) NO: 223)NO: 224) NO: 61) NO: 225) NO: 226) tgacaggt (SEQ ID NO: 218)

The cells were separated into four groups: No ZFN control, TCRA ZFNonly, B2M ZFN only, and TCRA ZFN+B2M ZFN. By FACS analysis, the sets ofZFNs against TCRA alone (180 μg/μL ZFN mRNA) or B2M alone (180 μg/μL ofZFN mRNA) gave high rates of cleavage (96% CD3 marking for the TCRA ZFNsand 92% knockout of HLA marking for the B2M ZFNs (FIG. 4)). When thecells were treated with both types of ZFN pairs (both at 180 μg/μL), 82%of the cells lost both CD3 and HLA marking.

Similar groups of cells were also treated with variable amounts ofTCRA-specific ZFNs as shown (60-250 ug/uL) plus the B2M ZFN at 60ug/mL), and at days 10 and 14 were subjected to MiSeq deep sequencing(Illumina) and FACs analysis where the results are shown below in Table6. The results indicate that high rates of double knockout as detectedby NHEJ-mediated insertions and deletions were observed with these ZFNs.

TABLE 6 FACS and miSeq analysis on TCRA/B2M double knockouts FACS MiSeqD10 D14 D10 D14 ug/uL TCRA- B2M- DOUBLE- TCRA- B2M- DOUBLE- TCRA- B2M-TCRA B2M- sham 2.3 2.9 2.1 3.0 3.8 2.1 0.6 1.8 0.2 1.4 TRAC 180 67.4 1.81.5 40.1 1.0 0.5 66.0 0.8 52.4 2.9 B2M 180 3.4 90.5 3.1 1.5 89.5 1.4 0.964.6 0.2 74.7 T180:B180 60.4 84.3 57.3 43.9 78.8 41.8 63.2 73.0 51.163.4 T240:B120 73.3 85.3 68.3 56.9 80.2 53.2 73.0 79.5 66.0 66.7T120:B240 79.4 80.5 71.2 70.6 73.9 63.2 79.0 72.1 69.2 61.3

Thus, the data demonstrate that double knockouts of B2M and TCRAinactivated both genes at or near the target and/or within 1-50 (e.g., 1to 10) base pairs (including between paired target sites) of the targetsequences and/or cleavage sites of the nucleases described herein(including the B2M sequence TCAAAT (site D in FIG. 1) and the TCRAsequence CCTTC, between the two target sequences for the SBS #55254/SBS#55248 TCRA-specific pair).

Example 5: Double Knockout of B2M and TCRA with Targeted Integration

Nucleases as described above (see, Example 4) were used to inactivateB2M and TCRA (see, Example 5) and to introduce, via targetedintegration, a donor (transgene) into either the TCRA or B2M locus. Inthis experiment, the TCRA-specific ZFN pair was SBS #55266/SBS #53853,comprising the sequence TTGAAA between the TCRA-specific ZFN targetsites (Table 5), and the B2M pair was SBS #57332/SBS #57327 (Table 1),comprising the sequence TCAAAT between the B2M-specific ZFN targetsites.

Briefly, T-Cells (AC-TC-006) were thawed and activated with CD3/28dynabeads (1:3 cells:bead ratio) in X-vivo15 T-cell culture media (day0). After two days in culture (day 2), an AAV donor (comprising a GFPtransgene and homology arms to the TCRA or B2M gene) was added to thecell culture, except control groups without donor were also maintained.The following day (day 3), TCRA and B2M ZFNs were added via mRNAdelivery in the following 5 Groups:

(a) Group 1 (TCRA and B2M ZFNs only, no donor): TCRA 120 ug/mL: B2M only60 ug/mL;(b) Group 2 (TCRA and B2M ZFNs and donor with TCRA homology arms): TCRA120 ug/mL; B2M 60 ug/mL and AAV (TCRA-hPGK-eGFP-Clone E2) 1E5vg/cell;(c) Group 3 (TCRA and B2M ZFNs and donor with TCRA homology arms): TCRA120 ug/mL; B2M 60 ug/mL; and AAV (TCRA-hPGK-eGFP-Clone E2) 3E4vg/cell;(d) Group 4 (TCRA and B2M ZFNs and donor with B2M homology arms): TCRA120 ug/mL; B2M 60 ug/mL and AAV (pAAV B2M site D hPGK GFP) 1E5vg/cell(e) Group 5 (TCRA and B2M ZFNs and donor with B2M homology arms): TCRA120 ug/mL; B2M 60 ug/mL and AAV (pAAV B2M site D hPGK GFP) 3E4vg/cell.All experiments were conducted at 3e7 cells/ml cell density using theprotocol as described in U.S. Patent Publication No. 2017/0137845(extreme cold shock) and were cultured to cold shock at 30° C. overnightpost electroporation.

The following day (day 4), cells were diluted to 0.5e6 cells/ml andtransferred to cultures at 37° C. Three days later (day 7), cellsdiluted to 0.5e6 cells/ml again. After three and seven more days inculture (days 10 and 14, respectively), cells were harvested for FACSand MiSeq analysis (diluted to 0.5e6 cells/ml).

As shown in FIG. 5, GFP expression indicated that target integration wassuccessful and that genetically modified cells comprising B2M and TCRAmodifications (insertions and/or deletions) within the nuclease sites(or within 1 to 50 base pairs of the nuclease target sites, includingwithin the TTGAAA and TCAAAT and/or between paired target sites) wereobtained.

Experiments are also performed in which a CAR transgene is integratedinto the B2M and/or TCRA locus to created double B2M/TCRA knockouts thatexpress a CAR.

All patents, patent applications and publications mentioned herein arehereby incorporated by reference in their entirety.

Although disclosure has been provided in some detail by way ofillustration and example for the purposes of clarity of understanding,it will be apparent to those skilled in the art that various changes andmodifications can be practiced without departing from the spirit orscope of the disclosure. Accordingly, the foregoing description andexamples should not be construed as limiting.

What is claimed is:
 1. An isolated lymphoid cell, induced pluripotentstem cell (iPSC), mesenchymal stem cell (MSC), hematopoietic stem cell(HSC) or progenitor cell in which expression of a beta 2 microglobulin(B2M) gene is partially or completely inactivated by an insertion and/ora deletion within TCAAAT (designated as site D in FIG. 1B) or TCAAATT(designated as cite C in FIG. 1B), of exon 2 of the B2M gene, whereinthe insertion and/or deletion is made by an exogenous fusion moleculecomprising a zinc finger protein (ZFP) or transcription activator-likeeffector (TALE) DNA-binding domain that binds to a target site as shownin SEQ ID NO: 8, 9, 10 or 11 and a cleavage domain or a cleavagehalf-domain; wherein when the cleavage site is TCAAAT, the target siteis SEQ ID NO: 8 or SEQ ID NO: 9; and wherein when the cleavage site isTCAAATT, the target site is SEQ ID NO: 9 or SEQ ID NO:10.
 2. The cell ofclaim 1, further comprising an inactivated T-cell receptor gene, PD1and/or CTLA4 gene.
 3. The cell of claim 1, further comprising atransgene encoding a chimeric antigen receptor (CAR), a transgeneencoding an Antibody-coupled T-cell Receptor (ACTR) and/or a transgeneencoding an engineered TCR.
 4. The cell of claim 1, wherein the cell isa T-cell.
 5. The cell of claim 1, wherein the cleavage half-domain is awild-type of engineered FokI cleavage half-domain.
 6. The cell of claim1, wherein the exogenous fusion molecule comprises a zinc fingernuclease (ZFN).
 7. The cell of claim 6, wherein the ZFN comprises a ZFPwith six zinc fingers designated F1-F6 in the order F1 to F6 for the ZFPdesigned as SBS57017, SBS57332, SBS57469 or BS57331 in a single row ofTable
 1. 8. The cell of claim 7, wherein the ZFN is used as part of aZFN pair, each ZFN of the pair comprising a ZFP with five or six zincfingers designated F1-F5 or F1-F6 in the order F1-F5 or F1-F6 shown in asingle row of Table 1, and wherein the ZFN is as follows: SBS57017 andSBS57327; SBS57017 and SBS57328; SBS57332 and SBS57327; SBS57469 andSBS57327; SBS57469 and SBS57328; or SBS57331 and SBS57326.
 9. The cellof claim 1, wherein the exogenous fusion molecule comprises a TALEprotein with the repeat variable diresidues (RVDs) for the TALEdesignated as 103076, 10377, 103079, 103081, 103083, 103085, or 103087shown in a single row of Table 2B.
 10. A pharmaceutical compositioncomprising a cell according to claim
 1. 11. A fusion molecule comprisinga DNA-binding domain that binds to exon 2 of a B2M gene and a cleavagedomain or cleavage half-domain, wherein the DNA-binding domain comprisesa ZFP with six zinc fingers designated F1-F6 in the order F1-F6 for theZFP designated as SBS57017, SBS57332, SBS57469 or SBS57331 in a singlerow of Table 1; or a TALE protein with the repeat variable diresiduesfor the TALE designated as 103076, 103077, 103079, 103081, 103083,103085, or 103087 s shown in a single row of Table 2B.
 12. Apolynucleotide encoding the fusion molecule of claim
 11. 13. Thepolynucleotide of claim 12, wherein the polynucleotide is a viralvector, a plasmid or mRNA.
 14. The cell of claim 2, further comprising atransgene encoding a chimeric antigen receptor (CAR), a transgeneencoding an Antibody-coupled T-cell Receptor (ACTR) and/or a transgeneencoding an engineered TCR.
 15. The cell of claim 2, wherein the cell isa T-cell.
 16. The cell of claim 2, wherein the cleavage half-domain is awild-type of engineered FokI cleavage half-domain.
 17. The cell of claim2, wherein the exogenous fusion molecule comprises a zinc fingernuclease (ZFN).
 18. The cell of claim 17, wherein the ZFN comprises aZFP with six zinc fingers designated F1-F6 in the order F1 to F6 for theZFP designed as SBS57017, SBS57332, SBS57469 or BS57331 in a single rowof Table
 1. 19. The cell of claim 18, wherein the ZFN is used as part ofa ZFN pair, each ZFN of the pair comprising a ZFP with five or six zincfingers designated F1-F5 or F1-F6 in the order F1-F5 or F1-F6 shown in asingle row of Table 1, and wherein the ZFN is as follows: SBS57017 andSBS57327; SBS57017 and SBS57328; SBS57332 and SBS57327; SBS57469 andSBS57327; SBS57469 and SBS57328; or SBS57331 and SBS57326.
 20. The cellof claim 19, wherein the exogenous fusion molecule comprises a TALEprotein with the repeat variable diresidues (RVDs) for the TALEdesignated as 103076, 10377, 103079, 103081, 103083, 103085, or 103087shown in a single row of Table 2B.